Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015254.1 Kokia drynarioides strain JFW-HI SEQ_130299, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1276691
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 890 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:881612 original size:87 final size:88
Alignment explanation
Indices: 881507--881670 Score: 242
Period size: 87 Copynumber: 1.9 Consensus size: 88
881497 CCCAGTTTTT
* * *
881507 TTCCAAAAATTACATTTTTACCCTCTAACTTCCAAAAATTTCATTTTGACC-CTAATTTTTCCAA
1 TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCTC-AATTTTTCCAA
881571 AAATTA-CATTTTTACCCTTGAAC
65 AAATTACCATTTTTACCCTTGAAC
** * *
881594 TTCCAAAAATTATGTTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCTCGATTTTTCCCAA
1 TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCTCAATTTTTCCAAA
881659 AATTACCATTTT
66 AATTACCATTTT
881671 ACCGCCAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
87 61 0.90
88 7 0.10
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (88 bp):
TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCTCAATTTTTCCAAA
AATTACCATTTTTACCCTTGAAC
Found at i:881627 original size:58 final size:58
Alignment explanation
Indices: 881507--881699 Score: 171
Period size: 58 Copynumber: 3.3 Consensus size: 58
881497 CCCAGTTTTT
* * **
881507 TTCCAAAAATTACATTTTTACCCTCT-AACTTCCAAAAATT-TCATTTTGA-CCCTAATTT
1 TTCCAAAAATTACATTTTTACCCT-TGAACTTCCAAAAATTAT-ATTTTTACCCCCAA-AC
*
881565 TTCCAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTATGTTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTATATTTTTACCCCCAAAC
* * * ** * * *
881623 TTCCAAAAATTCCATTTTGA-CCTCGATTTTTCCCAAAATTACCA-TTTTACCGCCAAAC
1 TTCCAAAAATTACATTTTTACCCTTGA-ACTTCCAAAAATTA-TATTTTTACCCCCAAAC
* *
881681 TTCCAAAAACTCCATTTTT
1 TTCCAAAAATTACATTTTT
881700 TATCCCAATT
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
57 6 0.05
58 102 0.89
59 6 0.05
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
TTCCAAAAATTACATTTTTACCCTTGAACTTCCAAAAATTATATTTTTACCCCCAAAC
Found at i:881655 original size:29 final size:29
Alignment explanation
Indices: 881507--881699 Score: 124
Period size: 29 Copynumber: 6.7 Consensus size: 29
881497 CCCAGTTTTT
*
881507 TTCCAAAAATTACATTTTTACCCTCTA-AC
1 TTCCAAAAATTACATTTTTA-CCTCGATAC
* * * **
881536 TTCCAAAAATTTCATTTTGACC-CTAATTT
1 TTCCAAAAATTACATTTTTACCTC-GATAC
*
881565 TTCCAAAAATTACATTTTTACCCTTGA-AC
1 TTCCAAAAATTACATTTTTA-CCTCGATAC
** * * *
881594 TTCCAAAAATTATGTTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCTCGATAC
* * **
881623 TTCCAAAAATTCCATTTTGACCTCGATTT
1 TTCCAAAAATTACATTTTTACCTCGATAC
* * * *
881652 TTCCCAAAATTACCA-TTTTACCGCCAAAC
1 TTCCAAAAATTA-CATTTTTACCTCGATAC
* *
881681 TTCCAAAAACTCCATTTTT
1 TTCCAAAAATTACATTTTT
881700 TATCCCAATT
Statistics
Matches: 121, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
27 1 0.01
28 8 0.07
29 107 0.88
30 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCTCGATAC
Found at i:881682 original size:87 final size:87
Alignment explanation
Indices: 881507--881699 Score: 239
Period size: 87 Copynumber: 2.2 Consensus size: 87
881497 CCCAGTTTTT
* * *
881507 TTCCAAAAATTACATTTTTACCCTCTAACTTCCAAAAATTTCATTTTGACCCTAATTTTTCCAAA
1 TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAAA
**
881572 AATTACATTTTTACCCTTGAAC
66 AATTACATTTTTACCCTCAAAC
** * *
881594 TTCCAAAAATTATGTTTTTACCCCCAAACTTCCAAAAATTCCATTTTGA-CCTCGATTTTTCCCA
1 TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCCT-AATTTTTCCAA
881658 AAATTACCA-TTTTACCGC-CAAAC
65 AAATTA-CATTTTTACC-CTCAAAC
* *
881681 TTCCAAAAACTCCATTTTT
1 TTCCAAAAATTACATTTTT
881700 TATCCCAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
86 3 0.03
87 84 0.93
88 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (87 bp):
TTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAAA
AATTACATTTTTACCCTCAAAC
Found at i:881707 original size:87 final size:85
Alignment explanation
Indices: 881507--881721 Score: 213
Period size: 87 Copynumber: 2.4 Consensus size: 85
881497 CCCAGTTTTT
* *
881507 TTCCAAAAATTACA-TTTTTACCCTCTAACTTCCAAAAATTTCATTTTGACCCTAATTTTTCCAA
1 TTCCAAAAA-T-CATTTTTTACCC-CAAACTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAA
**
881571 AAATTACATTTTTACCCTTGAAC
63 AAATTACATTTTTACCCTCAAAC
* * *
881594 TTCCAAAAATTATGTTTTTACCCCCAAACTTCCAAAAATTCCATTTTGA-CCTCGATTTTTCCCA
1 TTCCAAAAATCAT-TTTTTA-CCCCAAACTTCCAAAAATTCCATTTTGACCCT-AATTTTTCCAA
881658 AAATTACCA-TTTTACCGC-CAAAC
63 AAATTA-CATTTTTACC-CTCAAAC
* **
881681 TTCCAAAAACTCCATTTTTTATCCCAATTTTTCCAAAAATT
1 TTCCAAAAA-T-CATTTTTTACCCCAA-ACTTCCAAAAATT
881722 ACTATATTAC
Statistics
Matches: 108, Mismatches: 11, Indels: 17
0.79 0.08 0.12
Matches are distributed among these distances:
85 1 0.01
86 4 0.04
87 77 0.71
88 24 0.22
89 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (85 bp):
TTCCAAAAATCATTTTTTACCCCAAACTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAAAAA
TTACATTTTTACCCTCAAAC
Found at i:881717 original size:58 final size:59
Alignment explanation
Indices: 881609--881733 Score: 157
Period size: 58 Copynumber: 2.1 Consensus size: 59
881599 AAAATTATGT
* *
881609 TTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCTCGATTTTTCCC-AAAATTACCA
1 TTTTACCCCCAAACTTCCAAAAACTCCATTTTGACCTCAATTTTTCCCAAAAATTACCA
* * *
881667 TTTTACCGCCAAACTTCCAAAAACTCCATTTTTTATCC-CAATTTTT-CCAAAAATTACTA
1 TTTTACCCCCAAACTTCCAAAAACTCCA-TTTTGA-CCTCAATTTTTCCCAAAAATTACCA
*
881726 TATTACCC
1 TTTTACCC
881734 TCGGATGTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 28 0.49
59 27 0.47
60 2 0.04
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.36
Consensus pattern (59 bp):
TTTTACCCCCAAACTTCCAAAAACTCCATTTTGACCTCAATTTTTCCCAAAAATTACCA
Found at i:881786 original size:30 final size:30
Alignment explanation
Indices: 881739--881814 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
881729 TACCCTCGGA
*
881739 TGTCTAAAATT-CCATTTTTAACCCTAAAG
1 TGTCCAAAATTACCATTTTTAACCCTAAAG
* **
881768 T-TCCCAAAATTACCA-TTTTACCCCTCGAG
1 TGT-CCAAAATTACCATTTTTAACCCTAAAG
881797 TGTCCAAAATTACCATTT
1 TGTCCAAAATTACCATTT
881815 AACCCACGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 32 0.82
30 6 0.15
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.36
Consensus pattern (30 bp):
TGTCCAAAATTACCATTTTTAACCCTAAAG
Found at i:881816 original size:57 final size:56
Alignment explanation
Indices: 881711--881819 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 56
881701 ATCCCAATTT
* *
881711 TTCCAAAAATTACTATATTACCCTCGGATGTCTAAAATTCCATTTTTAACCCTAAAG
1 TTCCAAAAATTACCATATTACCCTCGGATGTCCAAAATTCCA-TTTTAACCCTAAAG
* *
881768 TTCCCAAAATTACCATTTTACCCCTC-GAGTGTCCAAAATTACCA-TTTAACCC
1 TTCCAAAAATTACCATATTA-CCCTCGGA-TGTCCAAAATT-CCATTTTAACCC
881820 ACGGGTATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 27 0.60
58 15 0.33
59 3 0.07
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (56 bp):
TTCCAAAAATTACCATATTACCCTCGGATGTCCAAAATTCCATTTTAACCCTAAAG
Found at i:881831 original size:28 final size:29
Alignment explanation
Indices: 881771--881835 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
881761 CCTAAAGTTC
* * *
881771 CCAAAATTACCATTTTACCCCTCGAGTGT
1 CCAAAATTACCATTTTAACCCACGAGTAT
*
881800 CCAAAATTACCA-TTTAACCCACGGGTAT
1 CCAAAATTACCATTTTAACCCACGAGTAT
881828 CCAAAATT
1 CCAAAATT
881836 CACTCTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (29 bp):
CCAAAATTACCATTTTAACCCACGAGTAT
Found at i:883012 original size:16 final size:16
Alignment explanation
Indices: 882988--883018 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
882978 TAAGAATTTT
*
882988 GTTTTAAGAATTGTGG
1 GTTTCAAGAATTGTGG
883004 GTTTCAAGAATTGTG
1 GTTTCAAGAATTGTG
883019 TTTGGATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (16 bp):
GTTTCAAGAATTGTGG
Found at i:883637 original size:12 final size:12
Alignment explanation
Indices: 883622--883646 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
883612 CAAAAAAAAA
883622 AAAATCTTAAAG
1 AAAATCTTAAAG
883634 AAAATCTTAAAG
1 AAAATCTTAAAG
883646 A
1 A
883647 TACACCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATCTTAAAG
Found at i:887746 original size:40 final size:40
Alignment explanation
Indices: 887697--887892 Score: 223
Period size: 42 Copynumber: 4.8 Consensus size: 40
887687 CTCGCTCAGG
* * * *
887697 GCCTACTAAGTCGTAGCTTGAATTATATCACCGGCTCATA
1 GCCTGCTAAGCCGAAGCTTGAATTATATCACCGACTCATA
* *
887737 GCCTGCTAAGCCGAAGCTTGAATTATATCACTGGCTCATA
1 GCCTGCTAAGCCGAAGCTTGAATTATATCACCGACTCATA
* *
887777 GCCTGCTAAGCTGAAGCTTGGATTATACATCACCGACTCATA
1 GCCTGCTAAGCCGAAGCTTGAATTAT--ATCACCGACTCATA
* * *
887819 TCCTGCTAAACCGAAGCTT-AGATTATACATCATCGACTCATA
1 GCCTGCTAAGCCGAAGCTTGA-ATTAT--ATCACCGACTCATA
* *
887861 GCCTACTAAGTCGAAGCTTGAATTATATCACC
1 GCCTGCTAAGCCGAAGCTTGAATTATATCACC
887893 ACAACTCATT
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
40 65 0.49
42 68 0.51
43 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (40 bp):
GCCTGCTAAGCCGAAGCTTGAATTATATCACCGACTCATA
Found at i:889671 original size:46 final size:50
Alignment explanation
Indices: 889621--889724 Score: 135
Period size: 50 Copynumber: 2.2 Consensus size: 50
889611 TATGGTCTAA
* * *
889621 TACTAGTTATGCACTTGGA-CA-A-TATTT-TAGTTATCATGTGGTGTAC
1 TACTAATTATGCACTTGGATAATATTATTTGTAGTAATCATGTGGTGTAC
*
889667 TACTAATTATGTACTTGGATAATATTATTTGTAGTAATCATGTGGTGTAC
1 TACTAATTATGCACTTGGATAATATTATTTGTAGTAATCATGTGGTGTAC
*
889717 TTCTAATT
1 TACTAATT
889725 TGTAATATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 17 0.35
47 1 0.02
48 1 0.02
49 5 0.10
50 25 0.51
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (50 bp):
TACTAATTATGCACTTGGATAATATTATTTGTAGTAATCATGTGGTGTAC
Found at i:889800 original size:46 final size:46
Alignment explanation
Indices: 889725--889820 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
889715 ACTTCTAATT
* ** * *
889725 TGTAATATTAGTTATGCACTTGGACAATATTGTAGCTATCATGTGG
1 TGTAATACTAGTTATGCACTTAAAAAATATTGTAGCTATCATGCGG
*
889771 TGTAATACTAGTTATGCACTTAAAAAATATTGTAGTTATCATGCGG
1 TGTAATACTAGTTATGCACTTAAAAAATATTGTAGCTATCATGCGG
889817 TGTA
1 TGTA
889821 CTATTAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (46 bp):
TGTAATACTAGTTATGCACTTAAAAAATATTGTAGCTATCATGCGG
Found at i:890207 original size:14 final size:15
Alignment explanation
Indices: 890190--890230 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
890180 TCTCTTAAAA
*
890190 AAAAATCATTTTTC-
1 AAAAATTATTTTTCT
890204 AAAAATTA-TTTTCT
1 AAAAATTATTTTTCT
890218 AAAAATTATTTTT
1 AAAAATTATTTTT
890231 AATTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 15 0.62
15 4 0.17
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAAATTATTTTTCT
Found at i:894214 original size:24 final size:24
Alignment explanation
Indices: 894187--894233 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
894177 GTATTTATAG
*
894187 TTTGATTAATACTTAATGAACTTT
1 TTTGAATAATACTTAATGAACTTT
*
894211 TTTGAATAATACTTAATTAACTT
1 TTTGAATAATACTTAATGAACTT
894234 AATTGATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTGAATAATACTTAATGAACTTT
Found at i:894239 original size:24 final size:24
Alignment explanation
Indices: 894188--894239 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
894178 TATTTATAGT
* **
894188 TTGATTAATACTTAATGAACTTTT
1 TTGAATAATACTTAATGAACTTAA
*
894212 TTGAATAATACTTAATTAACTTAA
1 TTGAATAATACTTAATGAACTTAA
894236 TTGA
1 TTGA
894240 TCATGATTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
TTGAATAATACTTAATGAACTTAA
Found at i:895101 original size:10 final size:10
Alignment explanation
Indices: 895086--895110 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
895076 TTCTCCAAAT
895086 TAAGTTTATA
1 TAAGTTTATA
895096 TAAGTTTATA
1 TAAGTTTATA
895106 TAAGT
1 TAAGT
895111 CTTTCTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (10 bp):
TAAGTTTATA
Found at i:916377 original size:24 final size:22
Alignment explanation
Indices: 916350--916394 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
916340 CTGTAAAATA
916350 GAAAGAAAACAAAAAAACAAAAGG
1 GAAA-AAAACAAAAAAA-AAAAGG
* *
916374 GAAATATACAAAAAAAAAAAG
1 GAAAAAAACAAAAAAAAAAAG
916395 AAATGTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.76, C:0.07, G:0.13, T:0.04
Consensus pattern (22 bp):
GAAAAAAACAAAAAAAAAAAGG
Found at i:917708 original size:21 final size:21
Alignment explanation
Indices: 917647--917708 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
917637 TTGTTGTTTA
*
917647 TTTATTTATTTTA-T-CTTTATT
1 TTTATTT-TTTTAGTACTTT-TG
917668 TTTATTTTTTT-GTTTA-TTTTG
1 TTTATTTTTTTAG--TACTTTTG
917689 TTTATTTTTTTAGTACTTTT
1 TTTATTTTTTTAGTACTTTT
917709 ATTTCATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
20 6 0.18
21 23 0.68
22 5 0.15
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (21 bp):
TTTATTTTTTTAGTACTTTTG
Found at i:917709 original size:38 final size:38
Alignment explanation
Indices: 917627--917712 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 38
917617 AATTCAATCT
917627 CTTTTATTGTTTGTTGTTTATTTATTTATTTTATCTTTA
1 CTTTTATT-TTTGTTGTTTATTTATTTATTTTATCTTTA
* *
917666 TTTTTATTTTT-TTGTTTATTTTGTTTATTTT-T-TTAGTA
1 CTTTTATTTTTGTTGTTTA-TTTATTTATTTTATCTT--TA
917704 CTTTTATTT
1 CTTTTATTT
917713 CATGTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
36 2 0.05
37 8 0.20
38 24 0.59
39 7 0.17
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (38 bp):
CTTTTATTTTTGTTGTTTATTTATTTATTTTATCTTTA
Found at i:917910 original size:4 final size:4
Alignment explanation
Indices: 917901--917947 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
917891 TTGTATTATT
* * * *
917901 TTTA TTTA TTTA TTTA TTTA TTTC TTT- TTTG TCTA TGTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
917948 AAATTTTTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:917921 original size:22 final size:22
Alignment explanation
Indices: 917865--917946 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
917855 TATCATCATT
917865 TTTA-TTATATTATTTTTATTTA
1 TTTATTTAT-TTATTTTTATTTA
* *
917887 ATTGTTGTA-TTATTTTTATTTA
1 TTTATT-TATTTATTTTTATTTA
* *
917909 TTTATTTATTTATTTCTTTTTTG
1 TTTATTTATTTATTT-TTATTTA
* *
917932 TCTATGTATTTATTT
1 TTTATTTATTTATTT
917947 AAAATTTTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.04
22 25 0.52
23 19 0.40
24 2 0.04
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTATTTATTTATTTTTATTTA
Found at i:923189 original size:33 final size:33
Alignment explanation
Indices: 923147--923213 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
923137 TAGATAGGGG
923147 AATGAAGAAGGGAATCTATCAAAATTCGTCCTT
1 AATGAAGAAGGGAATCTATCAAAATTCGTCCTT
923180 AATGAAGAAGGGAATCTATCAAAATTCGTCCTT
1 AATGAAGAAGGGAATCTATCAAAATTCGTCCTT
923213 A
1 A
923214 CGCCCTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (33 bp):
AATGAAGAAGGGAATCTATCAAAATTCGTCCTT
Found at i:924631 original size:15 final size:15
Alignment explanation
Indices: 924613--924643 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
924603 AAGAAGGGAG
924613 AGAAAAGAAAATAAA
1 AGAAAAGAAAATAAA
*
924628 AGAAAAGAACATAAA
1 AGAAAAGAAAATAAA
924643 A
1 A
924644 AAGAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.06
Consensus pattern (15 bp):
AGAAAAGAAAATAAA
Found at i:925747 original size:100 final size:100
Alignment explanation
Indices: 925633--926015 Score: 369
Period size: 100 Copynumber: 3.8 Consensus size: 100
925623 AACTACAATG
* * **
925633 GCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAGGAT-AAGGCTACAACATTGAATCCTATACC
1 GCAAATCTTATCTCCTTAAAGTTGCAGTAGAGCAAGATGAA-GCTACAACATCAAATCCTATACC
* * *
925697 TATAAATTTGCAGTGGGTCGGATTAAAGCTATAG-AA
65 CATAAAATTGCAGTGGGTCGAATTAAAGCTA-AGAAA
* * * *
925733 GCAAATCTTATCTCCCTGAAGATGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATACCC
1 GCAAATCTTATCTCCTTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATACCC
* * *
925798 CTAAAATTGTAGTGGGTCGAATTAAAGCTACGAAA
66 ATAAAATTGCAGTGGGTCGAATTAAAGCTAAGAAA
* * * * * *
925833 GCAAATCTTATCTCTTTAAAGTTGCAGTGGAGTAAGATGAAGCTACGACATCAAATCTTATATCC
1 GCAAATCTTATCTCCTTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATACCC
* * * * ** *
925898 TTAAAGTTACTGTGTATC-AGATTAAAGCTACGAAA
66 ATAAAATTGCAGTGGGTCGA-ATTAAAGCTAAGAAA
** * * * *
925933 GCAAATCTTTATCT-CTCTAAAGTTGTTGTAGAGCAAGATGAAGCTACTACACCAAAGCTTATAC
1 GCAAATC-TTATCTCCT-TAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATAC
* * *
925997 CCCTAAAGTTACAGTGGGT
64 CCATAAAATTGCAGTGGGT
926016 AGGATTGAAA
Statistics
Matches: 236, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
99 2 0.01
100 172 0.73
101 62 0.26
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (100 bp):
GCAAATCTTATCTCCTTAAAGTTGCAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATACCC
ATAAAATTGCAGTGGGTCGAATTAAAGCTAAGAAA
Found at i:925902 original size:50 final size:50
Alignment explanation
Indices: 925633--926013 Score: 200
Period size: 50 Copynumber: 7.6 Consensus size: 50
925623 AACTACAATG
* * * * * *
925633 GCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAGGATAAGGCTACAACA
1 GCAAATCTTATATCCTTAAAGTTGCAGTGGAGTAAGATAAAGCTACGACA
*** * * ** *
925683 TTGAATCCTATA-CCTATAAATTTGCAGTGG-GTCGGATTAAAGCTATAGA-A
1 GCAAATCTTATATCCT-TAAAGTTGCAGTGGAGTAAGA-TAAAGCTA-CGACA
* * * * * * * *
925733 GCAAATCTTATCTCCCTGAAGATGCAGTAGAGCAAGATGAAGCTACAACA
1 GCAAATCTTATATCCTTAAAGTTGCAGTGGAGTAAGATAAAGCTACGACA
* * * * * * *
925783 TCAAATCTTATACCCCTAAAATTGTAGTGG-GTCGAA-TTAAAGCTACGAAA
1 GCAAATCTTATATCCTTAAAGTTGCAGTGGAGT--AAGATAAAGCTACGACA
* * *
925833 GCAAATCTTATCTCTTTAAAGTTGCAGTGGAGTAAGATGAAGCTACGACA
1 GCAAATCTTATATCCTTAAAGTTGCAGTGGAGTAAGATAAAGCTACGACA
* * * * * *
925883 TCAAATCTTATATCCTTAAAGTTACTGTGTA-TCAGATTAAAGCTACGAAA
1 GCAAATCTTATATCCTTAAAGTTGCAGTGGAGTAAGA-TAAAGCTACGACA
** * * * *
925933 GCAAATCTT-TATCTCTCTAAAGTTGTTGTAGAGCAAGATGAAGCTACTACA
1 GCAAATCTTATATC-CT-TAAAGTTGCAGTGGAGTAAGATAAAGCTACGACA
* * * * *
925984 CCAAAGCTTATACCCCTAAAGTTACAGTGG
1 GCAAATCTTATATCCTTAAAGTTGCAGTGG
926014 GTAGGATTGA
Statistics
Matches: 238, Mismatches: 78, Indels: 30
0.69 0.23 0.09
Matches are distributed among these distances:
49 19 0.08
50 174 0.73
51 39 0.16
52 6 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (50 bp):
GCAAATCTTATATCCTTAAAGTTGCAGTGGAGTAAGATAAAGCTACGACA
Found at i:925923 original size:200 final size:201
Alignment explanation
Indices: 925633--926003 Score: 480
Period size: 200 Copynumber: 1.9 Consensus size: 201
925623 AACTACAATG
* **
925633 GCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAGGATAAGGCTACAACATTGAATCCTATACCT
1 GCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAAGATAAGGCTACAACATCAAATCCTATACCT
* * * * *
925698 ATAAATTTGCAGTGGGTCGGATTAAAGCTATAG-AAGCAAATC-TTATCTCCCTGAAGATGCAGT
66 ATAAAGTTACAGTGGATCAGATTAAAGCTA-AGAAAGCAAATCTTTATCTCCCTAAAGATGCAGT
* *
925761 AGAGCAAGATGAAGCTACAACATCAAATCTTATACCCCTAAAATTGTAGTGGGTCGAATTAAAGC
130 AGAGCAAGATGAAGCTACAACACCAAAGCTTATACCCCTAAAATTGTAGTGGGTCGAATTAAAGC
925826 TACGAAA
195 TACGAAA
* * * * *
925833 GCAAATCTTATCTCTTTAAAGTTGCAGTGGAGTAAGATGAA-GCTACGACATCAAATCTTATATC
1 GCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAAGAT-AAGGCTACAACATCAAATCCTATA-C
* * * * * **
925897 CT-TAAAGTTACTGTGTATCAGATTAAAGCTACGAAAGCAAATCTTTATCTCTCTAAAGTTGTTG
64 CTATAAAGTTACAGTGGATCAGATTAAAGCTAAGAAAGCAAATCTTTATCTCCCTAAAGATGCAG
*
925961 TAGAGCAAGATGAAGCTACTACACCAAAGCTTATACCCCTAAA
129 TAGAGCAAGATGAAGCTACAACACCAAAGCTTATACCCCTAAA
926004 GTTACAGTGG
Statistics
Matches: 144, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
199 1 0.01
200 83 0.58
201 60 0.42
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (201 bp):
GCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAAGATAAGGCTACAACATCAAATCCTATACCT
ATAAAGTTACAGTGGATCAGATTAAAGCTAAGAAAGCAAATCTTTATCTCCCTAAAGATGCAGTA
GAGCAAGATGAAGCTACAACACCAAAGCTTATACCCCTAAAATTGTAGTGGGTCGAATTAAAGCT
ACGAAA
Found at i:926038 original size:201 final size:200
Alignment explanation
Indices: 925616--926056 Score: 482
Period size: 201 Copynumber: 2.2 Consensus size: 200
925606 AAGTTGCAAT
* * *
925616 GGATTGAAACTACA-ATGGCAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAGGATAAGGCTACA
1 GGATTGAAACTACAGA-AGCAAATCTTATCTCTTTAAAGTTGCAGTCGAGCAAGATAAGGCTACA
** * * * * *
925680 ACATTGAATCCTATACCTATAAATTTGCAGTGGGTCGGATTAAAGCTATAGAAGCAAATCTTATC
65 ACATCAAATCCTATACCTATAAAGTTACAGTGGATCAGATTAAAGCTAGAGAAGCAAATCTTATC
* * * **
925745 TCCCTGAAGATGCAGTAGAGCAAGATGAAGCTACAACATCAAATCTTATACCCCTAAAATTGTAG
130 TCCCTAAAGATGCAGTAGAGCAAGATGAAGCTACAACACCAAAGCTTATACCCCTAAAATTACAG
*
925810 TGGGTC
195 TGGGTA
* * *
925816 GAATT-AAAGCTAC-GAAAGCAAATCTTATCTCTTTAAAGTTGCAGTGGAGTAAGATGAA-GCTA
1 GGATTGAAA-CTACAG-AAGCAAATCTTATCTCTTTAAAGTTGCAGTCGAGCAAGAT-AAGGCTA
* * * *
925878 CGACATCAAATCTTATATCCT-TAAAGTTACTGTGTATCAGATTAAAGCTACGA-AAGCAAATCT
63 CAACATCAAATCCTATA-CCTATAAAGTTACAGTGGATCAGATTAAAGCTA-GAGAAGCAAATC-
* * ** * *
925941 TTATCTCTCTAAAGTTGTTGTAGAGCAAGATGAAGCTACTACACCAAAGCTTATACCCCTAAAGT
125 TTATCTCCCTAAAGATGCAGTAGAGCAAGATGAAGCTACAACACCAAAGCTTATACCCCTAAAAT
926006 TACAGTGGGTA
190 TACAGTGGGTA
* *
926017 GGATTGAAATTACAGAAGCAAATCCTATCT-TTCTAAAGTT
1 GGATTGAAACTACAGAAGCAAATCTTATCTCTT-TAAAGTT
926057 ACGGTGAAGC
Statistics
Matches: 199, Mismatches: 32, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
199 3 0.02
200 93 0.47
201 99 0.50
202 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (200 bp):
GGATTGAAACTACAGAAGCAAATCTTATCTCTTTAAAGTTGCAGTCGAGCAAGATAAGGCTACAA
CATCAAATCCTATACCTATAAAGTTACAGTGGATCAGATTAAAGCTAGAGAAGCAAATCTTATCT
CCCTAAAGATGCAGTAGAGCAAGATGAAGCTACAACACCAAAGCTTATACCCCTAAAATTACAGT
GGGTA
Found at i:928134 original size:3 final size:3
Alignment explanation
Indices: 928126--928162 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
928116 TCATGATTGA
928126 ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
928163 CATCATCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:928167 original size:3 final size:3
Alignment explanation
Indices: 928161--928195 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
928151 TATTATTATT
928161 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
928196 TTTTGTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:928241 original size:19 final size:19
Alignment explanation
Indices: 928194--928256 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
928184 CATCATCATC
928194 ATTT-TTGTTATATTATTTTT
1 ATTTATTGTTATATTA--TTT
928214 ATTTAATTGTTATATTATTT
1 ATTT-ATTGTTATATTATTT
*
928234 ATTTATTGTTCAT-GTATTT
1 ATTTATTGTT-ATATTATTT
928253 ATTT
1 ATTT
928257 CAAATTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 15 0.38
20 13 0.33
22 11 0.28
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (19 bp):
ATTTATTGTTATATTATTT
Found at i:930714 original size:103 final size:104
Alignment explanation
Indices: 930534--930740 Score: 362
Period size: 103 Copynumber: 2.0 Consensus size: 104
930524 TATAGGAGTC
* * *
930534 GCCACAATCTTTTTTATTTGGTACGATTCGATCACTAAAAAATGTTTAAAATTCATTTTGAAAAA
1 GCCACAATATTTTTTATTTGGTACGATTCGATCACTAAAAAACGTTTAAAATCCATTTTGAAAAA
*
930599 TATTTTGGTTTTCGAAATCCAGAAAATGAGTTTGGGATT
66 TATTTTGGTTTTCGAAATCCAAAAAATGAGTTTGGGATT
*
930638 GCCACAATATTTTTTATTTGGTACGATTCGATCACT-AAAAACGTTTAAAATCCGTTTTGAAAAA
1 GCCACAATATTTTTTATTTGGTACGATTCGATCACTAAAAAACGTTTAAAATCCATTTTGAAAAA
930702 TATTTTGGTTTTCGAAATCCAAAAAATGAGTTTGGGATT
66 TATTTTGGTTTTCGAAATCCAAAAAATGAGTTTGGGATT
930741 CGATTACGTG
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 63 0.64
104 35 0.36
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (104 bp):
GCCACAATATTTTTTATTTGGTACGATTCGATCACTAAAAAACGTTTAAAATCCATTTTGAAAAA
TATTTTGGTTTTCGAAATCCAAAAAATGAGTTTGGGATT
Found at i:931411 original size:10 final size:11
Alignment explanation
Indices: 931396--931424 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
931386 CAAAGAATCG
931396 AAAAAAAA-TA
1 AAAAAAAATTA
931406 AAAAAAAATTA
1 AAAAAAAATTA
931417 AAAAAAAA
1 AAAAAAAA
931425 GAGGGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:931535 original size:60 final size:59
Alignment explanation
Indices: 931471--931630 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 59
931461 AGAATTTTGG
* * *
931471 GGGTCAAAACATAATTATAAAAAAGTTTGAGGGTTAAAATGTAATTTT--AGAAAAGTTTAA
1 GGGTCAAAATATAATTTTAAAAAAGTTT-AGGGTTAAAATGTAATTTTCAAG-AAA-TATAA
931531 GGGTCAAAATATAATTTTAAAAAAGTTTAGGGGTTAAAATGTAATTTTCAAGAAATATAA
1 GGGTCAAAATATAATTTTAAAAAAGTTTA-GGGTTAAAATGTAATTTTCAAGAAATATAA
* *
931591 GGGTCAAAATATAATTTTTAATAAGTTTAAGGGTTAAAAT
1 GGGTCAAAATATAATTTTAAAAAAGTTT-AGGGTTAAAAT
931631 TTATTTTTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
59 1 0.01
60 84 0.92
61 4 0.04
62 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (59 bp):
GGGTCAAAATATAATTTTAAAAAAGTTTAGGGTTAAAATGTAATTTTCAAGAAATATAA
Found at i:931639 original size:30 final size:30
Alignment explanation
Indices: 931471--931639 Score: 162
Period size: 30 Copynumber: 5.6 Consensus size: 30
931461 AGAATTTTGG
* * * * *
931471 GGGTCAAAACATAATTATAAAAAAGTTTGA
1 GGGTTAAAATATAATTTTTAAAAAGTTTAA
*
931501 GGGTTAAAATGTAA-TTTTAGAAAAGTTTAA
1 GGGTTAAAATATAATTTTTA-AAAAGTTTAA
* * *
931531 GGGTCAAAATATAATTTTAAAAAAGTTTAG
1 GGGTTAAAATATAATTTTTAAAAAGTTTAA
* * *
931561 GGGTTAAAATGTAATTTTCAAGAAA-TATAA
1 GGGTTAAAATATAATTTTTAA-AAAGTTTAA
* *
931591 GGGTCAAAATATAATTTTTAATAAGTTTAA
1 GGGTTAAAATATAATTTTTAAAAAGTTTAA
* *
931621 GGGTTAAAATTTATTTTTT
1 GGGTTAAAATATAATTTTT
931640 TTGTGAAGTT
Statistics
Matches: 112, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
29 5 0.04
30 100 0.89
31 7 0.06
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.37
Consensus pattern (30 bp):
GGGTTAAAATATAATTTTTAAAAAGTTTAA
Found at i:933343 original size:123 final size:123
Alignment explanation
Indices: 933121--934051 Score: 1229
Period size: 123 Copynumber: 7.6 Consensus size: 123
933111 ATCCGCTTCT
* *
933121 ATTGAGCTTTGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTGAT
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
* * * * *
933186 TGTTTAATCCACTTCTTTGTATCTCATCAAGAAGATGAGGGTTTGAAGTTTCGCTGAC
66 TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
* *
933244 ATTGAGCTTCACTTCATTATTTTGGTCTACTTCTCTGTATCTCATCGGGAAGATGACCGCTTGAT
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
* *
933309 TGTTTGATCCACTTCTCTGTATCTCATCTGGAAGATGGGGGTTTGAAGTTTCACTCAC
66 TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
* * * * * *
933367 ATTGGGCTTTGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGAAAGATGATCACTTGAC
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
* *
933432 TGTTTGATCCACTTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTCACTGAC
66 TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
* * * * *
933490 ATTGAGCTTTGCTTCTTTATTTTGCTCTACTTCTCTGTATCTCATCAGGAAGAAGACCGCTCGAT
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
** * * *
933555 TGTTTGATATACTTCTTTGTATCTCATCAGGAAAATGGGGGTTTGAAGTTTCACTCAC
66 TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
* * * * * *
933613 ATTGAGCTTCACTTCATTATTTTGCTTTGCTTCTCTGTATCTAATCAGGAAGATGACTGCTTGAT
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
* **
933678 TGTTTGATCCACTTCTCTATATCTCATCAGGAAGATGGGGGTTTGAAGTTTCGTTGAC
66 TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
* * * *** *
933736 ATTGAGCTTCGCTTCATTATTTTGGTCTGCTTCTCTATATCTTATCAGGAAGATGATAACTCGAT
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
* ** *
933801 TGTTTGATCCACGTCTCTGTATCTCATCAAAAAGATGGGGGTTTGAAGTTTCACTCAC
66 TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
* * * * * * *
933859 ATTGAGCTTCACTTCATTGTTTTGGTTTGCTTCTCTGTATCTCATCAAGAAAATGACCTCTTCG-
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTT-GA
* * * * *
933923 TTGTCTGACCCACTTCTCTGTATCTTATCAAGAAGATGGGGTTTTGAAGTTTCACTCG-C
65 TTGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACT-GAC
* * * *
933982 ATTGAGCTTCGCTTTATTA-TTTGGTCTACTTCTCTGTATCTCATTAGGAAGAAGACCGCTTCAT
1 ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGA-
934046 TTGTTT
65 TTGTTT
934052 TGACCCGACC
Statistics
Matches: 702, Mismatches: 102, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
122 35 0.05
123 666 0.95
124 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (123 bp):
ATTGAGCTTCGCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTGAT
TGTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTGAC
Found at i:934340 original size:49 final size:49
Alignment explanation
Indices: 934280--934397 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 49
934270 CAGTCTGCTT
* * *
934280 CATCTTCAGGGTATAAGATTCATTGTTGCGGCCTAAATCTTTCCCTTCA
1 CATCTTTAGGGTATAAGATTCACTGTTGCGGCCTAAACCTTTCCCTTCA
* ** *
934329 CATCTTTAGGGTATAAGGTTCACTGTTGCGGCCTCGACCTTTCCTTTCA
1 CATCTTTAGGGTATAAGATTCACTGTTGCGGCCTAAACCTTTCCCTTCA
*
934378 TATCTTTAGGGT-TCAAGATT
1 CATCTTTAGGGTAT-AAGATT
934398 TGTCATTGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 1 0.02
49 58 0.98
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (49 bp):
CATCTTTAGGGTATAAGATTCACTGTTGCGGCCTAAACCTTTCCCTTCA
Found at i:937721 original size:30 final size:29
Alignment explanation
Indices: 937678--937851 Score: 111
Period size: 30 Copynumber: 6.2 Consensus size: 29
937668 AAAAAAGGTC
*
937678 AAAATGAAGTTTTGGAAAA-TTTTAGGGGTT
1 AAAATTAA-TTTTGGAAAAGTTTT-GGGGTT
*
937708 AAAAATTAATTTTGGAAAAGTTTTTGGGTT
1 -AAAATTAATTTTGGAAAAGTTTTGGGGTT
937738 AAAATCTAATTTTGGAAAA--------GTT
1 AAAAT-TAATTTTGGAAAAGTTTTGGGGTT
* *
937760 -AAATGTAATTTTAGAAAAG-TTTGGGGTC
1 AAAAT-TAATTTTGGAAAAGTTTTGGGGTT
* * * *
937788 AAAATTTAATTTTGGTAAAGTTTAGGAGTA
1 AAAA-TTAATTTTGGAAAAGTTTTGGGGTT
* *
937818 AAAATATAATTTTGAAAAAG-TTTGAGGTT
1 AAAAT-TAATTTTGGAAAAGTTTTGGGGTT
937847 AAAAT
1 AAAAT
937852 GTGATTTTTA
Statistics
Matches: 114, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
21 16 0.14
22 3 0.03
28 2 0.02
29 31 0.27
30 51 0.45
31 11 0.10
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (29 bp):
AAAATTAATTTTGGAAAAGTTTTGGGGTT
Found at i:937768 original size:21 final size:21
Alignment explanation
Indices: 937739--937780 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
937729 TTTTGGGTTA
*
937739 AAATCTAATTTTGGAAAAGTT
1 AAATCTAATTTTAGAAAAGTT
*
937760 AAATGTAATTTTAGAAAAGTT
1 AAATCTAATTTTAGAAAAGTT
937781 TGGGGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (21 bp):
AAATCTAATTTTAGAAAAGTT
Found at i:937797 original size:29 final size:28
Alignment explanation
Indices: 937760--937851 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
937750 TGGAAAAGTT
* *
937760 AAATGTAATTTTAGAAAAGTTTGGGGTCA
1 AAATATAATTTT-GAAAAGTTTGGGGTAA
* * *
937789 AAATTTAATTTTGGTAAAGTTTAGGAGTAA
1 AAATATAATTTT-GAAAAGTTT-GGGGTAA
* *
937819 AAATATAATTTTGAAAAAGTTTGAGGTTA
1 AAATATAATTTTG-AAAAGTTTGGGGTAA
937848 AAAT
1 AAAT
937852 GTGATTTTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (28 bp):
AAATATAATTTTGAAAAGTTTGGGGTAA
Found at i:937798 original size:50 final size:50
Alignment explanation
Indices: 937710--937809 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
937700 TAGGGGTTAA
* * *
937710 AAATTAATTTTGGAAAAGTTTTTGGGTTAAAATCTAATTTTGGAAAAGTT
1 AAATTAATTTTAGAAAAGTTTTGGGGTCAAAATCTAATTTTGGAAAAGTT
* *
937760 AAATGTAATTTTAGAAAAG-TTTGGGGTCAAAATTTAATTTTGGTAAAGTT
1 AAAT-TAATTTTAGAAAAGTTTTGGGGTCAAAATCTAATTTTGGAAAAGTT
937810 TAGGAGTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 31 0.70
51 13 0.30
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (50 bp):
AAATTAATTTTAGAAAAGTTTTGGGGTCAAAATCTAATTTTGGAAAAGTT
Found at i:937822 original size:80 final size:81
Alignment explanation
Indices: 937679--937839 Score: 202
Period size: 80 Copynumber: 2.0 Consensus size: 81
937669 AAAAAGGTCA
* * * * * *
937679 AAATGAAGTTTTGGAAAATTTTAGGGGTTAAAAATTAATTTTGGAAAAGTTTTTGGGTTAAAATC
1 AAATGAAGTTTTAGAAAAGTTTAGGGGTCAAAAATTAATTTTGGAAAAGTTTTAGGGTAAAAATA
*
937744 TAATTTTGGAAAAGTT
66 TAATTTTGAAAAAGTT
* *
937760 AAATGTAA-TTTTAGAAAAGTTT-GGGGTCAAAATTTAATTTTGGTAAAG-TTTAGGAGTAAAAA
1 AAATG-AAGTTTTAGAAAAGTTTAGGGGTCAAAAATTAATTTTGGAAAAGTTTTAGG-GTAAAAA
937822 TATAATTTTGAAAAAGTT
64 TATAATTTTGAAAAAGTT
937840 TGAGGTTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
79 5 0.07
80 45 0.65
81 17 0.25
82 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.39
Consensus pattern (81 bp):
AAATGAAGTTTTAGAAAAGTTTAGGGGTCAAAAATTAATTTTGGAAAAGTTTTAGGGTAAAAATA
TAATTTTGAAAAAGTT
Found at i:938335 original size:20 final size:21
Alignment explanation
Indices: 938300--938338 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
938290 CTGATCTCCA
938300 GACCGTCACTTGCCCGCTGCC
1 GACCGTCACTTGCCCGCTGCC
*
938321 GACCGTCGC-TGCCCGCTG
1 GACCGTCACTTGCCCGCTG
938339 TTGTGCACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.08, C:0.46, G:0.28, T:0.18
Consensus pattern (21 bp):
GACCGTCACTTGCCCGCTGCC
Found at i:945416 original size:20 final size:21
Alignment explanation
Indices: 945377--945421 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
945367 AATTTTGGAA
* *
945377 TTTTAAAAATATTTTGAATT-
1 TTTTAAAAATATATTAAATTC
*
945397 TTTTAAAATTATATTAAATTC
1 TTTTAAAAATATATTAAATTC
945418 TTTT
1 TTTT
945422 TTTTGTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTAAAAATATATTAAATTC
Found at i:945520 original size:9 final size:9
Alignment explanation
Indices: 945502--945539 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
945492 TATCAATCTG
945502 TTATTCGAA
1 TTATTCGAA
*
945511 TTATTTGAA
1 TTATTCGAA
945520 TTATTC-AA
1 TTATTCGAA
945528 GTTATTCGAA
1 -TTATTCGAA
945538 TT
1 TT
945540 GTAAAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (9 bp):
TTATTCGAA
Found at i:945628 original size:14 final size:14
Alignment explanation
Indices: 945609--945638 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
945599 TATTTCGAAT
945609 AATTCAAATAACTC
1 AATTCAAATAACTC
*
945623 AATTCAATTAACTC
1 AATTCAAATAACTC
945637 AA
1 AA
945639 AATTTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTCAAATAACTC
Found at i:946049 original size:53 final size:54
Alignment explanation
Indices: 945926--946050 Score: 182
Period size: 53 Copynumber: 2.3 Consensus size: 54
945916 TAAATATTTT
* * *
945926 TAAAATTTTAAATTAATAAAAGTAAAATTATACTTTGATTCTCCCTAAAAATGA
1 TAAAATTTTAAATTAATAAAAGTAAAATTACACTTTGATCCTCCCTAAAAATAA
*
945980 TAAAATTTTAAATTAAT-AAAGATAAAATTACACTTTGA-CCTCCCTAAAATTAA
1 TAAAATTTTAAATTAATAAAAG-TAAAATTACACTTTGATCCTCCCTAAAAATAA
*
946033 TAAAATTTTAATTTAATA
1 TAAAATTTTAAATTAATA
946051 TTTTAAAAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
53 32 0.50
54 32 0.50
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.38
Consensus pattern (54 bp):
TAAAATTTTAAATTAATAAAAGTAAAATTACACTTTGATCCTCCCTAAAAATAA
Found at i:946659 original size:13 final size:14
Alignment explanation
Indices: 946630--946667 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
946620 GTTTTTCATC
946630 TATTTAAAATATTA
1 TATTTAAAATATTA
*
946644 TATTTTAAAT-TTA
1 TATTTAAAATATTA
946657 TA-TTAAAATAT
1 TATTTAAAATAT
946668 GTTGGACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTAAAATATTA
Found at i:948277 original size:20 final size:20
Alignment explanation
Indices: 948238--948278 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
948228 ATACATGAAA
*
948238 TTAAAAAAATAACTTTTAAT
1 TTAAAAAAATAACTTATAAT
948258 TTAAAGAAAATAA-TTATAAT
1 TTAAA-AAAATAACTTATAAT
948278 T
1 T
948279 ATCTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAAAAAATAACTTATAAT
Found at i:951445 original size:15 final size:14
Alignment explanation
Indices: 951414--951452 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
951404 TACTGTTTAC
**
951414 CATTTATTTTTTTG
1 CATTTATTTTTAAG
951428 CATTTATATTTTAAG
1 CATTTAT-TTTTAAG
951443 CATTTATTTT
1 CATTTATTTT
951453 CTCATACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (14 bp):
CATTTATTTTTAAG
Found at i:952014 original size:23 final size:23
Alignment explanation
Indices: 951976--952030 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
951966 TCCCTTGCAC
951976 TTCTATCG--ATACTTTGATGGG
1 TTCTATCGATATACTTTGATGGG
951997 TTCTATCGATATACTTTGATGGG
1 TTCTATCGATATACTTTGATGGG
952020 TTCTATCGATA
1 TTCTATCGATA
952031 CCAAATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 8 0.25
23 24 0.75
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.44
Consensus pattern (23 bp):
TTCTATCGATATACTTTGATGGG
Found at i:963884 original size:406 final size:405
Alignment explanation
Indices: 963133--963950 Score: 1519
Period size: 406 Copynumber: 2.0 Consensus size: 405
963123 TAATTATTTT
963133 ATTTTGTATATTTTGATATATCCATTTATTCGTATTTTATTTTTTTAAGAAGAAATTTATTCATA
1 ATTTTGTATATTTTGATATATCCATTTATTCGTATTTTATTTTTTTAAGAAGAAATTTATTCATA
*
963198 TTTTATTATTTTAATATTAATATTTATGAATAATATTTTTATTTTAATAAAATTTTTGGTTAAAT
66 TTTTATTAATTTAATATTAATATTTATGAATAATATTTTTATTTTAATAAAATTTTTGGTTAAAT
*
963263 AAATTTACTAAATAAAAGATTTACCATTCTTATAAACAACAGTTGTATCTACCTAAAAAAAATAT
131 AAATTTACTAAATAAAAGATTTACCATTCTTATAAACAACAGTTGTATCTACCTAAAAAAAAAAT
963328 ATATTCTAATTCTATTAAAATACTTTGAAAATGGGTGGGTTATTTTTTTGCTTGAGTAAACAGTT
196 ATATTCTAATTCTATTAAAATACTTTGAAAATGGGTGGGTTATTTTTTTGCTTGAGTAAACAGTT
* *
963393 GGAAATTTTGTTTAAAAAATTGGTAGTTGCTTTTTATTTATTTTGAAAGCAAGAATTGGTGGTCT
261 GAAAATTTTGTTTAAAAAATTGGTAGTTGCTTTTTATTTATTTTGAAAGCAAGAATTGATGGTCT
*
963458 GTTTCATTTTTCCAATAAAGCAATCAGAAGTTGTTAAAGGTATGAAAGTGGGTGGTTGTGTTAAA
326 ATTTCATTTTTCCAATAAAGCAATCAGAAGTTGTTAAAGGTATGAAAGTGGGTGGTTGTGTTAAA
*
963523 GAAATTTTAATGTGA
391 GAAACTTTAATGTGA
963538 ATTTTGTATATTTTGATATATCCATTTATTCGTATTTTATTTTTTTTAAGAAGAAATTTATTCAT
1 ATTTTGTATATTTTGATATATCCATTTATTCGTATTTTA-TTTTTTTAAGAAGAAATTTATTCAT
963603 ATTTTATTAATTTAATATTAATATTTATGAATAATATTTTTATTTTAATAAAATTTTTGGTTAAA
65 ATTTTATTAATTTAATATTAATATTTATGAATAATATTTTTATTTTAATAAAATTTTTGGTTAAA
* * *
963668 TAAATTTATTTAATAAAAGATTTACCATTCTTATAAATAACAGTTGTATCTACCTAAAAAAAAAA
130 TAAATTTACTAAATAAAAGATTTACCATTCTTATAAACAACAGTTGTATCTACCTAAAAAAAAAA
*
963733 TATATTCTAATTCTATTAAAATATTTTGAAAATGGGTGGGTTATTTTTTTGCTTGAGTAAACAGT
195 TATATTCTAATTCTATTAAAATACTTTGAAAATGGGTGGGTTATTTTTTTGCTTGAGTAAACAGT
* *
963798 TGAAAATTTTGTTTAAAAAATTGGTAGTTGTTTTTTATTTTTTTTGAAAGCAAGAATTGATGGTC
260 TGAAAATTTTGTTTAAAAAATTGGTAGTTGCTTTTTATTTATTTTGAAAGCAAGAATTGATGGTC
963863 TATTTCATTTTTCCAATAAAGCAATCAGAAGTTGTTAAAGGTATGAAAGTGGGTGGTTGTGTTAA
325 TATTTCATTTTTCCAATAAAGCAATCAGAAGTTGTTAAAGGTATGAAAGTGGGTGGTTGTGTTAA
963928 AGAAACTTTAATGTGA
390 AGAAACTTTAATGTGA
963944 ATTTTGT
1 ATTTTGT
963951 TTTGTTAGAA
Statistics
Matches: 400, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
405 39 0.10
406 361 0.90
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (405 bp):
ATTTTGTATATTTTGATATATCCATTTATTCGTATTTTATTTTTTTAAGAAGAAATTTATTCATA
TTTTATTAATTTAATATTAATATTTATGAATAATATTTTTATTTTAATAAAATTTTTGGTTAAAT
AAATTTACTAAATAAAAGATTTACCATTCTTATAAACAACAGTTGTATCTACCTAAAAAAAAAAT
ATATTCTAATTCTATTAAAATACTTTGAAAATGGGTGGGTTATTTTTTTGCTTGAGTAAACAGTT
GAAAATTTTGTTTAAAAAATTGGTAGTTGCTTTTTATTTATTTTGAAAGCAAGAATTGATGGTCT
ATTTCATTTTTCCAATAAAGCAATCAGAAGTTGTTAAAGGTATGAAAGTGGGTGGTTGTGTTAAA
GAAACTTTAATGTGA
Found at i:964456 original size:26 final size:25
Alignment explanation
Indices: 964427--964486 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
964417 ATACTTCGTG
964427 TTAT-TTTTTGAATATTTATGAATTTT
1 TTATATTTTT-AATATTTAT-AATTTT
* *
964453 TTATAATTTTTATTTTTTATAATTTT
1 TTAT-ATTTTTAATATTTATAATTTT
*
964479 TTAAATTT
1 TTATATTT
964487 ATTTGTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 4 0.14
26 13 0.45
27 7 0.24
28 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (25 bp):
TTATATTTTTAATATTTATAATTTT
Found at i:964469 original size:16 final size:16
Alignment explanation
Indices: 964448--964479 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
964438 ATATTTATGA
964448 ATTTTTTATAATTTTT
1 ATTTTTTATAATTTTT
964464 ATTTTTTATAATTTTT
1 ATTTTTTATAATTTTT
964480 TAAATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTATAATTTTT
Found at i:971032 original size:24 final size:24
Alignment explanation
Indices: 970999--971073 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
970989 ATACTGGTTA
970999 AACTCTATCTGGGCTCGAATGAGCT
1 AACT-TATCTGGGCTCGAATGAGCT
*
971024 AACTTATCTGGGCTCGTAA-GAACT
1 AACTTATCTGGGCTCG-AATGAGCT
* * *
971048 AACTTGTATGGGCTCGTATGAGCT
1 AACTTATCTGGGCTCGAATGAGCT
971072 AA
1 AA
971074 TTTTGTTTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.02
24 36 0.84
25 6 0.14
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (24 bp):
AACTTATCTGGGCTCGAATGAGCT
Found at i:971085 original size:25 final size:24
Alignment explanation
Indices: 971008--971094 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
970998 AAACTCTATC
* * *
971008 TGGGCTCGAATGAGCTAACTTATC
1 TGGGCTCGTATGAGCTAACTTGTA
* *
971032 TGGGCTCGTAAGAACTAACTTGTA
1 TGGGCTCGTATGAGCTAACTTGTA
* *
971056 TGGGCTCGTATGAGCTAATTTTGTT
1 TGGGCTCGTATGAGCTAA-CTTGTA
*
971081 TGGGCTTGTATGAG
1 TGGGCTCGTATGAG
971095 ATAAATTTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
24 35 0.67
25 17 0.33
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (24 bp):
TGGGCTCGTATGAGCTAACTTGTA
Found at i:973664 original size:15 final size:15
Alignment explanation
Indices: 973644--973673 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
973634 GATTAAAACG
973644 TAATTAAAATATTAA
1 TAATTAAAATATTAA
973659 TAATTAAAATATTAA
1 TAATTAAAATATTAA
973674 CAAAACATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTAAAATATTAA
Found at i:973869 original size:24 final size:24
Alignment explanation
Indices: 973837--973886 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
973827 ATAAACATAC
973837 AAAAGTATTATCAATTTCTTTAGT
1 AAAAGTATTATCAATTTCTTTAGT
*
973861 AAAAGTATTGTCAATTTCTTTAGT
1 AAAAGTATTATCAATTTCTTTAGT
973885 AA
1 AA
973887 TTGTTCTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
AAAAGTATTATCAATTTCTTTAGT
Found at i:975909 original size:22 final size:22
Alignment explanation
Indices: 975882--975925 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
975872 ATAAAATTAT
975882 TAAATA-TTAAAATAAAGTAAAA
1 TAAATATTTAAAA-AAAGTAAAA
*
975904 TAAATATTTAAAAAAATTAAAA
1 TAAATATTTAAAAAAAGTAAAA
975926 AATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATATTTAAAAAAAGTAAAA
Found at i:977286 original size:17 final size:19
Alignment explanation
Indices: 977246--977288 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
977236 ATACTTTTTT
*
977246 AATATTTTAATAATACACA
1 AATATTTTAATAACACACA
*
977265 CATATTTT-AT-ACACACA
1 AATATTTTAATAACACACA
977282 AATATTT
1 AATATTT
977289 AAACCCGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTTTAATAACACACA
Found at i:977450 original size:20 final size:19
Alignment explanation
Indices: 977418--977466 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
977408 TTCAATTATA
*
977418 ATTTAATTTCAAATAAAAG
1 ATTTTATTTCAAATAAAAG
* *
977437 ATTTTATTTACAAATCATAG
1 ATTTTATTT-CAAATAAAAG
977457 ATTTTATTTC
1 ATTTTATTTC
977467 TTTTACATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (19 bp):
ATTTTATTTCAAATAAAAG
Found at i:988496 original size:6 final size:6
Alignment explanation
Indices: 988473--988516 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
988463 TAAAGGCATA
* * * *
988473 TATATG TATTTT TATATG TATATG TATATT TATATG TACATG TA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TA
988517 CATTATACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (6 bp):
TATATG
Found at i:988496 original size:18 final size:18
Alignment explanation
Indices: 988473--988516 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
988463 TAAAGGCATA
*
988473 TATATGTATTTTTATATG
1 TATATGTATATTTATATG
988491 TATATGTATATTTATATG
1 TATATGTATATTTATATG
*
988509 TACATGTA
1 TATATGTA
988517 CATTATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (18 bp):
TATATGTATATTTATATG
Found at i:992925 original size:27 final size:27
Alignment explanation
Indices: 992887--992941 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
992877 AGGCTGGATC
992887 GAGTTGTGGCATCTTCTATGTTCCTCA
1 GAGTTGTGGCATCTTCTATGTTCCTCA
992914 GAGTTGTGGCATCTTCTATGTTCCTCA
1 GAGTTGTGGCATCTTCTATGTTCCTCA
992941 G
1 G
992942 CGACCATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (27 bp):
GAGTTGTGGCATCTTCTATGTTCCTCA
Found at i:995738 original size:20 final size:19
Alignment explanation
Indices: 995702--995741 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
995692 TTTAGGTTAA
**
995702 TTTTTTTTCTTATTTCTTT
1 TTTTTTTTCCGATTTCTTT
995721 TTTTTTTTCCGATATTCTTT
1 TTTTTTTTCCGAT-TTCTTT
995741 T
1 T
995742 CGTCCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTTTTTCCGATTTCTTT
Found at i:997825 original size:81 final size:81
Alignment explanation
Indices: 997687--997840 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 81
997677 TGCGAAGGAT
* * * * *
997687 AACGTTGCGATGTTGTAGAGGAATGTTGCGATGTTATGAAAGACAACGTTGCAACTTCACCCTTT
1 AACGTCGCGACGTTGTAGACGAATGTTGCGATATTATGAAAGACAACGTCGCAACTTCACCCTTT
997752 GAATTACAGTCCTTCG
66 GAATTACAGTCCTTCG
* * * ** *
997768 AACGTCGCGACGTTGTAGACGAATGTTGTGATATTGTGAAAGACAATGTCGTGACTTCGCCCTTT
1 AACGTCGCGACGTTGTAGACGAATGTTGCGATATTATGAAAGACAACGTCGCAACTTCACCCTTT
*
997833 GAGTTACA
66 GAATTACA
997841 ATATCGTGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (81 bp):
AACGTCGCGACGTTGTAGACGAATGTTGCGATATTATGAAAGACAACGTCGCAACTTCACCCTTT
GAATTACAGTCCTTCG
Found at i:1002335 original size:35 final size:35
Alignment explanation
Indices: 1002286--1002402 Score: 96
Period size: 35 Copynumber: 3.4 Consensus size: 35
1002276 TGATGTCCTA
* * * *
1002286 CTTAACATGTGAATCAAAAT-AAGATTTATGGCATG
1 CTTAACATGCGAATCAAAATCAA-AATAATAGCATG
* *
1002321 CTTAACATGCGAATCATAGTCAAAATAATAGCATG
1 CTTAACATGCGAATCAAAATCAAAATAATAGCATG
* * * **
1002356 CTTAACATGCGGATCATAATTAGTATAATA-CATG
1 CTTAACATGCGAATCAAAATCAAAATAATAGCATG
*
1002390 C-TCACATGCGAAT
1 CTTAACATGCGAAT
1002403 TGAAACATCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 10 0.15
34 5 0.07
35 51 0.75
36 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (35 bp):
CTTAACATGCGAATCAAAATCAAAATAATAGCATG
Found at i:1002706 original size:18 final size:17
Alignment explanation
Indices: 1002674--1002712 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1002664 GCTCAATAAG
1002674 CATTTTAAGCATATTTA
1 CATTTTAAGCATATTTA
*
1002691 CATTTCTAAGCTTATTTA
1 CATTT-TAAGCATATTTA
1002709 CATT
1 CATT
1002713 CATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (17 bp):
CATTTTAAGCATATTTA
Found at i:1002883 original size:48 final size:48
Alignment explanation
Indices: 1002827--1002986 Score: 142
Period size: 48 Copynumber: 3.1 Consensus size: 48
1002817 TTGTTGCATT
1002827 CATAAATAAAGTAGTGTTTTTAATTATGATTCATTGTTTGTTTTGTTG
1 CATAAATAAAGTAGTGTTTTTAATTATGATTCATTGTTTGTTTTGTTG
* *
1002875 CATAAATAAAGTTGTGTTTTTAACTATGCTTCATTATGCTTTATTGTTTGTTTTGTTG
1 CATAAATAAAGTAGTGTTTTTAATTATG----A-T-T-C---ATTGTTTGTTTTGTTG
* * *
1002933 CATTCATAAATAAAGTGGTG-TTTTAATTATGCTTCATTGATTGTTTTGTTG
1 ----CATAAATAAAGTAGTGTTTTTAATTATGATTCATTGTTTGTTTTGTTG
1002984 CAT
1 CAT
1002987 TCATTTTTCG
Statistics
Matches: 92, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
47 3 0.03
48 26 0.28
51 15 0.16
52 1 0.01
53 1 0.01
54 2 0.02
55 2 0.02
56 1 0.01
58 16 0.17
61 10 0.11
62 15 0.16
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.51
Consensus pattern (48 bp):
CATAAATAAAGTAGTGTTTTTAATTATGATTCATTGTTTGTTTTGTTG
Found at i:1002919 original size:110 final size:109
Alignment explanation
Indices: 1002709--1002986 Score: 387
Period size: 110 Copynumber: 2.5 Consensus size: 109
1002699 AGCTTATTTA
* * * * *
1002709 CATTCATAAAAAAAGTCGTGCTTTTATTTATGCA-TCATTGATAGTTTAGTTGCATTCATAAATA
1 CATTCATAAATAAAGTAGTG-TTTTAATTATG-ATTCATTGATTGTTTTGTTG----CATAAATA
* *
1002773 AAGTTGTGTTTTTAATTATGCTTCATTATGTTTTATTATTTGTTTTGTTG
60 AAGTTGTGTTTTTAACTATGCTTCATTATGCTTTATTATTTGTTTTGTTG
*
1002823 CATTCATAAATAAAGTAGTGTTTTTAATTATGATTCATTGTTTGTTTTGTTGCATAAATAAAGTT
1 CATTCATAAATAAAGTAGTG-TTTTAATTATGATTCATTGATTGTTTTGTTGCATAAATAAAGTT
*
1002888 GTGTTTTTAACTATGCTTCATTATGCTTTATTGTTTGTTTTGTTG
65 GTGTTTTTAACTATGCTTCATTATGCTTTATTATTTGTTTTGTTG
* *
1002933 CATTCATAAATAAAGTGGTGTTTTAATTATGCTTCATTGATTGTTTTGTTGCAT
1 CATTCATAAATAAAGTAGTGTTTTAATTATGATTCATTGATTGTTTTGTTGCAT
1002987 TCATTTTTCG
Statistics
Matches: 150, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
109 32 0.21
110 74 0.49
113 1 0.01
114 43 0.29
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (109 bp):
CATTCATAAATAAAGTAGTGTTTTAATTATGATTCATTGATTGTTTTGTTGCATAAATAAAGTTG
TGTTTTTAACTATGCTTCATTATGCTTTATTATTTGTTTTGTTG
Found at i:1003430 original size:117 final size:117
Alignment explanation
Indices: 1003224--1003461 Score: 350
Period size: 117 Copynumber: 2.0 Consensus size: 117
1003214 AAAATTCACA
* ** * * *
1003224 TATTCATTGGTCAGGTTTAATGGACAAAATACCAAAAGGTTCATATTGATTTTAAGTGACCATTC
1 TATTCATTGATCAGACTTAATGGACAAAATACCAAAAGGTTCACATTCATCTTAAGTGACCATTC
* *
1003289 GACTAGCCAAAGACCCTTTAATTGCCAACCACCAAGATGAGAGTTTTGTGAC
66 GACTAGCCAAAGACCCTTTAATTGCCAACAACCAAGATGAAAGTTTTGTGAC
* *
1003341 TATTCATTGATCAGACTTAATGGACGAAATACCAAAAGGTTCACATTCATCTTAAGTGACCATTT
1 TATTCATTGATCAGACTTAATGGACAAAATACCAAAAGGTTCACATTCATCTTAAGTGACCATTC
* ** *
1003406 GACTAGCCAAAGTCCCTTTAATTGCTGACAATCAAGATGAAAGTTTTGTGAC
66 GACTAGCCAAAGACCCTTTAATTGCCAACAACCAAGATGAAAGTTTTGTGAC
1003458 TATT
1 TATT
1003462 TGTGTGCTTC
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (117 bp):
TATTCATTGATCAGACTTAATGGACAAAATACCAAAAGGTTCACATTCATCTTAAGTGACCATTC
GACTAGCCAAAGACCCTTTAATTGCCAACAACCAAGATGAAAGTTTTGTGAC
Found at i:1003545 original size:63 final size:63
Alignment explanation
Indices: 1003446--1003571 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
1003436 ATCAAGATGA
*
1003446 AAGTTTTGTGACTATTTGTGTGCTTCATGCATTCATGTATAGTTAAGGTATTTAACTTCATGG
1 AAGTTTTGTGACTATTCGTGTGCTTCATGCATTCATGTATAGTTAAGGTATTTAACTTCATGG
*
1003509 AAGTTTTGTGACTATTCGTGTGCTTCATGCATTCATGTATAGTTAAGGTATTTAATTTCATGG
1 AAGTTTTGTGACTATTCGTGTGCTTCATGCATTCATGTATAGTTAAGGTATTTAACTTCATGG
1003572 TTGGTTTTGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (63 bp):
AAGTTTTGTGACTATTCGTGTGCTTCATGCATTCATGTATAGTTAAGGTATTTAACTTCATGG
Found at i:1006108 original size:22 final size:22
Alignment explanation
Indices: 1006073--1006114 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1006063 TATACAAGCA
* * *
1006073 ATATTACTTGAATAGTTATGAG
1 ATATTAATTAAATAATTATGAG
1006095 ATATTAATTAAATAATTATG
1 ATATTAATTAAATAATTATG
1006115 TTTCTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (22 bp):
ATATTAATTAAATAATTATGAG
Found at i:1009159 original size:27 final size:27
Alignment explanation
Indices: 1009115--1009169 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1009105 GATGAACTTC
* *
1009115 TTCACCGCTCAGATCTCTCAAATGGGT
1 TTCACCGCTCAAACCTCTCAAATGGGT
1009142 TTCACCGCTCAAACCTCTCAAATGGGT
1 TTCACCGCTCAAACCTCTCAAATGGGT
1009169 T
1 T
1009170 GTTGTTATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (27 bp):
TTCACCGCTCAAACCTCTCAAATGGGT
Found at i:1015744 original size:18 final size:19
Alignment explanation
Indices: 1015715--1015750 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1015705 CAATATCACT
1015715 TTGTGCGTGATATTATTGC
1 TTGTGCGTGATATTATTGC
1015734 TTGTG-GTGATATTATTG
1 TTGTGCGTGATATTATTG
1015751 TGAGGAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (19 bp):
TTGTGCGTGATATTATTGC
Found at i:1016214 original size:21 final size:22
Alignment explanation
Indices: 1016174--1016214 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1016164 TATTAATGGA
*
1016174 TGATTCTAGTGTTGTAAATAGT
1 TGATTCTAGTGATGTAAATAGT
*
1016196 TGATTTTAGTGAT-TAAATA
1 TGATTCTAGTGATGTAAATA
1016215 AAGGGTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (22 bp):
TGATTCTAGTGATGTAAATAGT
Found at i:1016785 original size:14 final size:14
Alignment explanation
Indices: 1016766--1016793 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1016756 ACTTTAATGT
1016766 ATTAAATGATTTAA
1 ATTAAATGATTTAA
1016780 ATTAAATGATTTAA
1 ATTAAATGATTTAA
1016794 TGATTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTAAATGATTTAA
Found at i:1030055 original size:27 final size:27
Alignment explanation
Indices: 1030005--1030056 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1029995 GGTACAAGAG
* * *
1030005 GTGGTGCCTACTTGATAGGTGGCACTA
1 GTGGTGCCTACCTGACAGGCGGCACTA
*
1030032 GTGGTGCCTACCTGCCAGGCGGCAC
1 GTGGTGCCTACCTGACAGGCGGCAC
1030057 CAAAGGTGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.15, C:0.27, G:0.35, T:0.23
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACTA
Found at i:1030083 original size:27 final size:27
Alignment explanation
Indices: 1030034--1030086 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1030024 TGGCACTAGT
*
1030034 GGTGCCTACCTGCCAGGCGGCACCAAA
1 GGTGCCTACCTGCCAGCCGGCACCAAA
* * *
1030061 GGTGCCTACTTGGCAGCCTGCACCAA
1 GGTGCCTACCTGCCAGCCGGCACCAA
1030087 TCCCATATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (27 bp):
GGTGCCTACCTGCCAGCCGGCACCAAA
Found at i:1033556 original size:25 final size:25
Alignment explanation
Indices: 1033509--1033556 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1033499 CTGTTTAAAT
**
1033509 TTGAATTTATTTAATAATTTTTATG
1 TTGAATTTATTTAATAAGGTTTATG
*
1033534 TTGAATTTATTTAATGAGGTTTA
1 TTGAATTTATTTAATAAGGTTTA
1033557 GCAAATGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (25 bp):
TTGAATTTATTTAATAAGGTTTATG
Found at i:1036061 original size:13 final size:13
Alignment explanation
Indices: 1036045--1036072 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1036035 TAATTTGTCA
1036045 TTTTAAAAAATAT
1 TTTTAAAAAATAT
1036058 TTTTAAAAAATAT
1 TTTTAAAAAATAT
1036071 TT
1 TT
1036073 AATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:1036085 original size:16 final size:17
Alignment explanation
Indices: 1036064--1036101 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1036054 ATATTTTTAA
1036064 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
1036080 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
*
1036097 CAAAT
1 AAAAT
1036102 GAATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:1036883 original size:17 final size:17
Alignment explanation
Indices: 1036861--1036894 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1036851 CTTACAATAA
*
1036861 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
1036878 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
1036895 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:1037161 original size:19 final size:19
Alignment explanation
Indices: 1037139--1037178 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1037129 GTAGCAGCAT
* *
1037139 GCAGCAGGGGTAACACACG
1 GCAGCAGAGGCAACACACG
*
1037158 GCAGCAGAGGCAGCACACG
1 GCAGCAGAGGCAACACACG
1037177 GC
1 GC
1037179 GAACGGCAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.38, T:0.03
Consensus pattern (19 bp):
GCAGCAGAGGCAACACACG
Found at i:1037246 original size:27 final size:27
Alignment explanation
Indices: 1037203--1037254 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1037193 ATTGGGACTA
1037203 GGTGCCGCCTAGTAGGTAAGCACCATT
1 GGTGCCGCCTAGTAGGTAAGCACCATT
*
1037230 GGTGCCGCCTA-TCAGGTAGGCACCA
1 GGTGCCGCCTAGT-AGGTAAGCACCA
1037255 CCCAAATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (27 bp):
GGTGCCGCCTAGTAGGTAAGCACCATT
Found at i:1037355 original size:16 final size:16
Alignment explanation
Indices: 1037315--1037349 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1037305 CAGTATTTTT
1037315 TTTAAA-AATTTATTA
1 TTTAAATAATTTATTA
1037330 TTTAAATAATTTATTA
1 TTTAAATAATTTATTA
1037346 TTTA
1 TTTA
1037350 TTTAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAATAATTTATTA
Found at i:1040221 original size:26 final size:26
Alignment explanation
Indices: 1040181--1040232 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1040171 GAGACGTAAG
* *
1040181 AAATTAAGATCAGAATATGAAATAAA
1 AAATTAACATCAGAATATAAAATAAA
*
1040207 AAATTAACATTAGAATATAAAATAAA
1 AAATTAACATCAGAATATAAAATAAA
1040233 TCACTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATTAACATCAGAATATAAAATAAA
Found at i:1040240 original size:26 final size:26
Alignment explanation
Indices: 1040192--1040241 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1040182 AATTAAGATC
* *
1040192 AGAATATGAAATAAAAAATTAACATT
1 AGAATATAAAATAAAAAACTAACATT
**
1040218 AGAATATAAAATAAATCACTAACA
1 AGAATATAAAATAAAAAACTAACA
1040242 AAAATCTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (26 bp):
AGAATATAAAATAAAAAACTAACATT
Found at i:1040353 original size:22 final size:22
Alignment explanation
Indices: 1040325--1040373 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1040315 AAGTGCATAG
1040325 ATTCACGATCACACAATAAAAC
1 ATTCACGATCACACAATAAAAC
*
1040347 ATTCACGATCACACCATAAAAC
1 ATTCACGATCACACAATAAAAC
1040369 ATTCA
1 ATTCA
1040374 AGTCTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (22 bp):
ATTCACGATCACACAATAAAAC
Found at i:1042221 original size:6 final size:6
Alignment explanation
Indices: 1042212--1042273 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
1042202 CAAATTTATT
**
1042212 TTTAAA TTTAAA TCTTTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA ---TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1042261 TTAAAA TTTAAA T
1 TTTAAA TTTAAA T
1042274 GGATTTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 7 0.16
6 32 0.71
9 6 0.13
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:1042249 original size:17 final size:15
Alignment explanation
Indices: 1042210--1042273 Score: 74
Period size: 17 Copynumber: 4.0 Consensus size: 15
1042200 TTCAAATTTA
1042210 TTTTTAAATTTAAAT
1 TTTTTAAATTTAAAT
*
1042225 CTTTTAAATTTAAAT
1 TTTTTAAATTTAAAT
1042240 TTGCTTTAAATTTAAAT
1 TT--TTTAAATTTAAAT
*
1042257 TTAATTAAAATTTAAAT
1 TT--TTTAAATTTAAAT
1042274 GGATTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
15 15 0.36
17 27 0.64
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTTTAAATTTAAAT
Found at i:1042390 original size:18 final size:18
Alignment explanation
Indices: 1042367--1042406 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1042357 CAAATAAACC
1042367 AATTACACCCCAAACCCA
1 AATTACACCCCAAACCCA
* * *
1042385 AATTACATCTCTAACCCA
1 AATTACACCCCAAACCCA
1042403 AATT
1 AATT
1042407 CACAAGTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (18 bp):
AATTACACCCCAAACCCA
Found at i:1043155 original size:80 final size:80
Alignment explanation
Indices: 1043056--1043215 Score: 266
Period size: 80 Copynumber: 2.0 Consensus size: 80
1043046 AACATGAATG
*
1043056 GGCAAAATCGAACTGATCTTTTTGGGATTCGAAAATAAAAACGTGTAAAGAACAAAGAAAGGGTT
1 GGCAAAATCGAACAGATCTTTTTGGGATTCGAAAATAAAAACGTGTAAAGAACAAAGAAAGGGTT
* *
1043121 GAGGTCTTCTTTAAA
66 AAGGTATTCTTTAAA
* * *
1043136 GGCAAAATCGAACAGATCTTTTTGGGTTTCGAAAATAAAAATGTTTAAAGAACAAAGAAAGGGTT
1 GGCAAAATCGAACAGATCTTTTTGGGATTCGAAAATAAAAACGTGTAAAGAACAAAGAAAGGGTT
1043201 AAGGTATTCTTTAAA
66 AAGGTATTCTTTAAA
1043216 ATCTGGGTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (80 bp):
GGCAAAATCGAACAGATCTTTTTGGGATTCGAAAATAAAAACGTGTAAAGAACAAAGAAAGGGTT
AAGGTATTCTTTAAA
Found at i:1044243 original size:59 final size:60
Alignment explanation
Indices: 1044176--1044466 Score: 342
Period size: 59 Copynumber: 4.9 Consensus size: 60
1044166 TTTGACCCCC
* * *
1044176 AACTTCCAAAGATTCCATTTTCGACCTCAAAACTTCCAAAAATCCCATTTATACCCTC-A
1 AACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGA
* * * * *
1044235 AACTTCCAAAAATCCCATTTT-TACCCCCAAACTTCCAAAAATTTCATTTTTGACCCT-GA
1 AACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTCCATTTTT-ACCCTCGA
* * * * *
1044294 AACTTCCAAAAATTCCATTTTCGACCCCAAAATTTCCAAAATTTACATTTTTATCCTCGA
1 AACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGA
* * * * *
1044354 AA-TTCCAAAAAATCCATTTTCGACTTCGAAACTCCCAAAAATTCCATTTTTAACCTCGA
1 AACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGA
* *
1044413 AACTTCAAAAAATTCCATTTT-TACCCTC-AAACTTCCAAAAATTCCATTTTTACC
1 AACTTCCAAAAATTCCATTTTCGA-CCTCAAAACTTCCAAAAATTCCATTTTTACC
1044467 AGCGAATGTC
Statistics
Matches: 196, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
58 24 0.12
59 124 0.63
60 48 0.24
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (60 bp):
AACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGA
Found at i:1044463 original size:29 final size:29
Alignment explanation
Indices: 1044176--1044515 Score: 303
Period size: 30 Copynumber: 11.5 Consensus size: 29
1044166 TTTGACCCCC
* *
1044176 AACTTCCAAAGATTCCATTTTCGA-CCTCAA
1 AACTTCCAAAAATTCCATTTT-TACCCTC-A
* *
1044206 AACTTCCAAAAATCCCATTTATACCCTCA
1 AACTTCCAAAAATTCCATTTTTACCCTCA
* *
1044235 AACTTCCAAAAATCCCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCTCA
* *
1044264 AACTTCCAAAAATTTCATTTTTGACCCTGA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCA
*
1044294 AACTTCCAAAAATTCCATTTTCGACCC-CAA
1 AACTTCCAAAAATTCCATTTT-TACCCTC-A
* * * *
1044324 AATTTCCAAAATTTACATTTTTATCCTCGA
1 AACTTCCAAAAATTCCATTTTTACCCTC-A
* * *
1044354 AA-TTCCAAAAAATCCATTTTCGA-CTTCGA
1 AACTTCCAAAAATTCCATTTT-TACCCTC-A
* *
1044383 AACTCCCAAAAATTCCATTTTTAACCTCGA
1 AACTTCCAAAAATTCCATTTTTACCCTC-A
*
1044413 AACTTCAAAAAATTCCATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTTACCCTCA
** *
1044442 AACTTCCAAAAATTCCATTTTTACCAGCG
1 AACTTCCAAAAATTCCATTTTTACCCTCA
* * *
1044471 AA-TGTCAAAAAATTCCATCTTTTAACCTTA
1 AACT-TCCAAAAATTCCAT-TTTTACCCTCA
*
1044501 AACTTTCCCAAAATT
1 AAC-TTCCAAAAATT
1044516 AGAATTTTGC
Statistics
Matches: 255, Mismatches: 43, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
28 1 0.00
29 116 0.45
30 129 0.51
31 8 0.03
32 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCA
Found at i:1044482 original size:59 final size:59
Alignment explanation
Indices: 1044176--1044515 Score: 286
Period size: 59 Copynumber: 5.7 Consensus size: 59
1044166 TTTGACCCCC
* * * * * *
1044176 AACTTCCAAAGATTCCATTTTCGA-CCTCAAAACTTCCAAAAATCCCATTTATACCCTC-A
1 AACTTCAAAAAATTCCATTTT-TACCCTC-AAACTTCCAAAAATTCCATTTTTAACCTCGA
* * * * *
1044235 AACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATTTCATTTTTGACC-CTGA
1 AACTTCAAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTC-GA
* * * * * *
1044294 AACTTCCAAAAATTCCATTTTCGACCC-CAAAATTTCCAAAATTTACATTTTTATCCTCGA
1 AACTTCAAAAAATTCCATTTT-TACCCTC-AAACTTCCAAAAATTCCATTTTTAACCTCGA
* * *
1044354 AA-TTCCAAAAAA-TCCATTTTCGA-CTTCGAAACTCCCAAAAATTCCATTTTTAACCTCGA
1 AACTT-CAAAAAATTCCATTTT-TACCCTC-AAACTTCCAAAAATTCCATTTTTAACCTCGA
*
1044413 AACTTCAAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTT-ACCAGCG-
1 AACTTCAAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACC-TCGA
* * *
1044471 AA-TGTCAAAAAATTCCATCTTTTAACCTTAAACTTTCCCAAAATT
1 AACT-TCAAAAAATTCCAT-TTTTACCCTCAAAC-TTCCAAAAATT
1044516 AGAATTTTGC
Statistics
Matches: 235, Mismatches: 31, Indels: 29
0.80 0.11 0.10
Matches are distributed among these distances:
57 2 0.01
58 43 0.18
59 130 0.55
60 59 0.25
61 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (59 bp):
AACTTCAAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGA
Found at i:1044514 original size:89 final size:84
Alignment explanation
Indices: 1044176--1044515 Score: 277
Period size: 89 Copynumber: 3.8 Consensus size: 84
1044166 TTTGACCCCC
* * * * * *
1044176 AACTTCCAAAGATTCCATTTTCGACCTCAAAACTTCCAAAAATCCCATTTATACCCTCAAACTTC
1 AACTTCCAAAAATTCCATTTT-TACC-C-GAA-TTCCAAAAATTCCATTTTTAACCTCAAACTTC
* *
1044241 CAAAAATCCCATTTTTACCCCCA
62 CAAAAATTCCATTTTTACCCTCA
* ** * *
1044264 AACTTCCAAAAATTTCATTTTTGACCCTGAAACTTCCAAAAATTCCATTTTCGACCCCAAAATTT
1 AACTTCCAAAAATTCCATTTTT-ACCC-G-AA-TTCCAAAAATTCCATTTTTAACCTC-AAACTT
* * *
1044329 CCAAAATTTACATTTTTATCCTCGA
61 CCAAAAATTCCATTTTTACCCTC-A
* * * *
1044354 AA-TTCCAAAAAATCCATTTTCGACTTCGAAACTCCCAAAAATTCCATTTTTAACCTCGAAACTT
1 AACTTCCAAAAATTCCATTTT-TAC-CCG-AA-TTCCAAAAATTCCATTTTTAACCTC-AAACTT
*
1044418 CAAAAAATTCCATTTTTACCCTCA
61 CCAAAAATTCCATTTTTACCCTCA
* *
1044442 AACTTCCAAAAATTCCATTTTTACCAGCGAATGTCAAAAAATTCCATCTTTTAACCTTAAACTTT
1 AACTTCCAAAAATTCCATTTTTACC--CGAAT-TCCAAAAATTCCAT-TTTTAACCTCAAAC-TT
*
1044507 CCCAAAATT
61 CCAAAAATT
1044516 AGAATTTTGC
Statistics
Matches: 201, Mismatches: 39, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
87 2 0.01
88 67 0.33
89 128 0.64
90 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (84 bp):
AACTTCCAAAAATTCCATTTTTACCCGAATTCCAAAAATTCCATTTTTAACCTCAAACTTCCAAA
AATTCCATTTTTACCCTCA
Found at i:1056516 original size:205 final size:205
Alignment explanation
Indices: 1056150--1056672 Score: 816
Period size: 205 Copynumber: 2.6 Consensus size: 205
1056140 GATTATCCAT
* * *
1056150 AAAC-AACGATGCGGTCATGTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAA-TCCACGCT
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACT-CACGCT
* *
1056213 CGATGTGAGCAAATCTTCGAATCCCAGCTTCCAGATAAGATACTGAGAAGCAAGGCGAAGCAATA
65 CGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAATA
* *
1056278 AAAGGTTAGCTTCCTGATAAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
130 AAAGGTTAGCTTCCTGATAAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
1056343 GAAGCGAATTG
195 GAAGCGAATTG
* *
1056354 AAACAAACGACGCGGTCATCTTCCTTATGAGATACTGACAAGAAGACCAAATCAAACTCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
* * * *
1056419 GATGTAAGCAAATCTTCAAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGTAATAA
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAATAA
* * * * *
1056484 AAGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTTTTCTTGATTAGATACAGAG
131 AAGGTTAGCTTCCTGATAAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
*
1056549 AAGTGAATTG
196 AAGCGAATTG
* *
1056559 AAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
* *
1056624 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAAATACTAAGAAG
66 GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAG
1056673 TGGACCAAAT
Statistics
Matches: 290, Mismatches: 27, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
204 4 0.01
205 285 0.98
206 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (205 bp):
AAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
GATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAAGGCGAAGCAATAA
AAGGTTAGCTTCCTGATAAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
AAGCGAATTG
Found at i:1056778 original size:158 final size:158
Alignment explanation
Indices: 1056490--1056811 Score: 547
Period size: 158 Copynumber: 2.0 Consensus size: 158
1056480 ATAAAAGGTT
* * * * * *
1056490 AGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTTTTCTTGATTAGATACAGAGAAGTGA
1 AGCTTCCTGATGAAATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGA
*
1056555 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCAC
66 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAAAAGACCAAATCAAACCCAC
1056620 GCTCGATGTGAGCAAATCTTCGAATCC-C
131 GCTCGATGTGAGCAAATCTTCGAA-CCTC
1056648 AGCTTCCTGATGAAATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGA
1 AGCTTCCTGATGAAATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGA
**
1056713 ATTGAAACAAACGACGTTGTCATCTTCCTGATGAGATATTGAGAAAAAGACCAAATCAAACCCAC
66 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAAAAGACCAAATCAAACCCAC
1056778 GCTCGATGTGAGCAAATCTTCGAACCTC
131 GCTCGATGTGAGCAAATCTTCGAACCTC
1056806 AGCTTC
1 AGCTTC
1056812 TTGAGAAGAC
Statistics
Matches: 154, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
157 2 0.01
158 152 0.99
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (158 bp):
AGCTTCCTGATGAAATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGA
ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAAAAGACCAAATCAAACCCAC
GCTCGATGTGAGCAAATCTTCGAACCTC
Found at i:1056950 original size:363 final size:363
Alignment explanation
Indices: 1056285--1056976 Score: 924
Period size: 363 Copynumber: 1.9 Consensus size: 363
1056275 ATAAAAGGTT
* * *
1056285 AGCTTCCTGATAAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
1 AGCTTCCTGATAAGATACTAAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGA
* * *
1056350 ATTGAAACAAACGACGCGGTCATCTTCCTTATGAGATACTGACAAGAAGACCAAATCAAACTCAC
66 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGACAAAAAGACCAAATCAAACCCAC
* *
1056415 GCTCGATGTAAGCAAATCTTCAAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGTA
131 GCTCGATGTAAGCAAATCTTCAAATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGGCGAAGCA
* * * ** * * * * *
1056480 ATAAAAGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTTTTCTTGATTAGATAC
196 ATAAAAGGTTAGCTTCCTGATGAAATACGAAGAAGTGAACCAAAACCATCTTCCTGATGAAATAC
** * *
1056545 AGAGAAGTGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAA
261 AGAGAAGTGAATCAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
1056610 TCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCC
326 TCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCC
*
1056648 AGCTTCCTGATGAA-ATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCG
1 AGCTTCCTGAT-AAGATACTAAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCG
** * *
1056712 AATTGAAACAAACGACGTTGTCATCTTCCTGATGAGATATTGAGAAAAAGACCAAATCAAACCCA
65 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGACAAAAAGACCAAATCAAACCCA
* * * *
1056777 CGCTCGATGTGAGCAAATCTTCGAA-CCTCAGCTTCTTGA-GAAGACACTGAGAAGCAGGTCGAA
130 CGCTCGATGTAAGCAAATCTTCAAATCC-CAGCTTCCTGATG-AGACACTGAGAAGCAGGGCGAA
* ** * *
1056840 GCAATACAAGGTTAGCTTCCTGATGAAATACGGGGAGGTGAACCAAAACCATCTTCCTGCTGAAA
193 GCAATAAAAGGTTAGCTTCCTGATGAAATACGAAGAAGTGAACCAAAACCATCTTCCTGATGAAA
** * * * * *
1056905 TACAGAGAAGT-AGATCAAAACAAGTGATATGGTCGTTTTCCTGATGAGATACTGAGAAGAAGGC
258 TACAGAGAAGTGA-ATCAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGAC
*
1056969 CAAGTCAA
322 CAAATCAA
1056977 TGAAACCAGA
Statistics
Matches: 281, Mismatches: 44, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
362 4 0.01
363 275 0.98
364 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (363 bp):
AGCTTCCTGATAAGATACTAAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGA
ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGACAAAAAGACCAAATCAAACCCAC
GCTCGATGTAAGCAAATCTTCAAATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGGCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAAATACGAAGAAGTGAACCAAAACCATCTTCCTGATGAAATAC
AGAGAAGTGAATCAAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCC
Found at i:1057346 original size:6 final size:6
Alignment explanation
Indices: 1057315--1057402 Score: 60
Period size: 6 Copynumber: 15.2 Consensus size: 6
1057305 TTTTATTGGG
* ** **
1057315 TTTAAA TTT--A TTCAAA TTTATT TTTAAA TTTAAA TTTATCT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA
**
1057362 TTTAAA TTT-TC TTTAAA TTTAAA TTT-AA -TTAAA TTTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA T
1057403 GGATTTAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
4 5 0.08
5 7 0.11
6 40 0.66
7 9 0.15
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:1057351 original size:18 final size:18
Alignment explanation
Indices: 1057328--1057388 Score: 97
Period size: 19 Copynumber: 3.4 Consensus size: 18
1057318 AAATTTATTC
1057328 AAATTTATTTTTAAATTT
1 AAATTTATTTTTAAATTT
1057346 AAATTTATCTTTTAAATTT
1 AAATTTAT-TTTTAAATTT
*
1057365 AAATTT-TCTTTAAATTT
1 AAATTTATTTTTAAATTT
1057382 AAATTTA
1 AAATTTA
1057389 ATTAAATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 15 0.38
18 9 0.22
19 16 0.40
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
AAATTTATTTTTAAATTT
Found at i:1057519 original size:18 final size:18
Alignment explanation
Indices: 1057496--1057535 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1057486 CAAATAAACC
1057496 AATTACACCCCAAACCCA
1 AATTACACCCCAAACCCA
* * *
1057514 AATTACATCTCTAACCCA
1 AATTACACCCCAAACCCA
1057532 AATT
1 AATT
1057536 CACAAGTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (18 bp):
AATTACACCCCAAACCCA
Found at i:1059202 original size:29 final size:29
Alignment explanation
Indices: 1059165--1059530 Score: 243
Period size: 30 Copynumber: 12.5 Consensus size: 29
1059155 TAGAAATCAT
* *
1059165 ATTTTGA-CCCTGAACTTCCAAAGATTCC
1 ATTTTGACCCCCGAACTTCCAAAAATTCC
*
1059193 ATTTTCGA-CCCCGAAACTTCC-AAAATCCC
1 ATTTT-GACCCCCG-AACTTCCAAAAATTCC
* *
1059222 ATTTTTACCCTCGAACTTCCAAAAA-TCC
1 ATTTTGACCCCCGAACTTCCAAAAATTCC
*
1059250 AATTTCT-ACCCCCGAACTTCCAAAAATTTC
1 -ATTT-TGACCCCCGAACTTCCAAAAATTCC
**
1059280 ATTTTTGACCCCAAAACTTCCAAAAATTCC
1 A-TTTTGACCCCCGAACTTCCAAAAATTCC
* *
1059310 ATTTTTGA-TCACGAAACTTCCAAAAATTCC
1 A-TTTTGACCCCCG-AACTTCCAAAAATTCC
** *
1059340 ATTTTAGA-CTTCGAAACTCCCAAAAATTCC
1 ATTTT-GACCCCCG-AACTTCCAAAAATTCC
* ** *
1059370 ATTTTTACCCCTAAAC-TCTCAAAAATTTCA
1 ATTTTGACCCCCGAACTTC-CAAAAA-TTCC
** *
1059400 ATTTTGACCCCAAAACTTCTAAAAATT-C
1 ATTTTGACCCCCGAACTTCCAAAAATTCC
* *
1059428 ATTTTTACCCCCAAACTTCCAAAAATTCC
1 ATTTTGACCCCCGAACTTCCAAAAATTCC
* * *
1059457 ATTTTTACCCCC-AAATGTCTAAAAATTCC
1 ATTTTGACCCCCGAACT-TCCAAAAATTCC
* * * *
1059486 ATCTTTTAACCTCGAACTTTCTC-ACAATTACC
1 AT-TTTGACCCCCGAAC-TTC-CAAAAATT-CC
1059518 ATTTT-ACCCCCGA
1 ATTTTGACCCCCGA
1059531 GTATCCAAAG
Statistics
Matches: 274, Mismatches: 42, Indels: 42
0.77 0.12 0.12
Matches are distributed among these distances:
28 43 0.16
29 92 0.34
30 120 0.44
31 14 0.05
32 5 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
ATTTTGACCCCCGAACTTCCAAAAATTCC
Found at i:1059211 original size:30 final size:29
Alignment explanation
Indices: 1059165--1059487 Score: 295
Period size: 30 Copynumber: 11.1 Consensus size: 29
1059155 TAGAAATCAT
* *
1059165 ATTTTGACCCTG-AACTTCCAAAGATTCC
1 ATTTTGACCCCGAAACTTCCAAAAATTCC
*
1059193 ATTTTCGACCCCGAAACTTCC-AAAATCCC
1 ATTTT-GACCCCGAAACTTCCAAAAATTCC
*
1059222 ATTTTTACCCTCG-AACTTCCAAAAA-TCC
1 ATTTTGACCC-CGAAACTTCCAAAAATTCC
*
1059250 AATTTCT-ACCCCCG-AACTTCCAAAAATTTC
1 -ATTT-TGA-CCCCGAAACTTCCAAAAATTCC
*
1059280 ATTTTTGACCCCAAAACTTCCAAAAATTCC
1 A-TTTTGACCCCGAAACTTCCAAAAATTCC
* *
1059310 ATTTTTGATCACGAAACTTCCAAAAATTCC
1 A-TTTTGACCCCGAAACTTCCAAAAATTCC
** *
1059340 ATTTTAGACTTCGAAACTCCCAAAAATTCC
1 ATTTT-GACCCCGAAACTTCCAAAAATTCC
* * *
1059370 ATTTTTACCCCTAAAC-TCTCAAAAATTTCA
1 ATTTTGACCCCGAAACTTC-CAAAAA-TTCC
* *
1059400 ATTTTGACCCCAAAACTTCTAAAAATT-C
1 ATTTTGACCCCGAAACTTCCAAAAATTCC
* *
1059428 ATTTTTACCCCCAAACTTCCAAAAATTCC
1 ATTTTGACCCCGAAACTTCCAAAAATTCC
* * *
1059457 ATTTTTACCCCCAAA-TGTCTAAAAATTCC
1 ATTTTGACCCCGAAACT-TCCAAAAATTCC
1059486 AT
1 AT
1059488 CTTTTAACCT
Statistics
Matches: 249, Mismatches: 29, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
28 44 0.18
29 96 0.39
30 107 0.43
31 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
ATTTTGACCCCGAAACTTCCAAAAATTCC
Found at i:1059424 original size:59 final size:58
Alignment explanation
Indices: 1059177--1059493 Score: 286
Period size: 59 Copynumber: 5.4 Consensus size: 58
1059167 TTTGACCCTG
* * * * * * *
1059177 AACTTCCAAAGATTCCATTTTCGACCCCGAAACTTCC-AAAATCCCATTTTTACCCTC-G
1 AACTTCCAAAAATTCCATTTT-TACCCCCAAACTTCCAAAAATTCAATTTTGACCC-CAA
* * *
1059235 AACTTCCAAAAA-TCCAATTTCTACCCCCGAACTTCCAAAAATTTCATTTTTGACCCCAA
1 AACTTCCAAAAATTCC-ATTTTTACCCCCAAACTTCCAAAAA-TTCAATTTTGACCCCAA
* * * * ** *
1059294 AACTTCCAAAAATTCCATTTTTGATCACGAAACTTCCAAAAATTCCATTTTAGACTTCGA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCAATTTT-GACCCCAA
* *
1059354 AACTCCCAAAAATTCCATTTTTACCCCTAAAC-TCTCAAAAATTTCAATTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTC-CAAAAA-TTCAATTTTGACCCCAA
* * * *
1059413 AACTTCTAAAAATT-CATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCAATTTTGACCCCAA
*
1059470 AA-TGTCTAAAAATTCCATCTTTTA
1 AACT-TCCAAAAATTCCAT-TTTTA
1059494 ACCTCGAACT
Statistics
Matches: 212, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.00
57 41 0.19
58 47 0.22
59 71 0.33
60 52 0.25
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCAATTTTGACCCCAA
Found at i:1071486 original size:59 final size:60
Alignment explanation
Indices: 1071399--1071616 Score: 239
Period size: 60 Copynumber: 3.7 Consensus size: 60
1071389 TTTTTTACCT
* * * *
1071399 AATTTAGTATTTGAACTTAACACCTTTTT-TTAATTTGTTACCTAAATTTTTTTTGGACTC
1 AATTTGGTACTTGAACTTGACA-CTTTTTCTTAATTTGGTACCTAAATTTTTTTTGGACTC
* * *
1071459 ATTTTGGTACTTGAACTTGTCACTTTTTCCTAATTTGGTACCTAAATTTTTTTT--ACTC
1 AATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAATTTTTTTTGGACTC
* * *
1071517 AATTTGGTA-TCTGAACTTAACATTTTTTTCCTAATTTGGTACCTAAA-TTTTTTTGGACTC
1 AATTTGGTACT-TGAACTTGACA-CTTTTTCTTAATTTGGTACCTAAATTTTTTTTGGACTC
** * * *
1071577 AATTTCATACCTGAACTTGGCATTTTTTCTTAATTTGGTA
1 AATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTA
1071617 AGCTTTTTTT
Statistics
Matches: 135, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
57 1 0.01
58 28 0.21
59 46 0.34
60 60 0.44
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (60 bp):
AATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAATTTTTTTTGGACTC
Found at i:1071532 original size:118 final size:114
Alignment explanation
Indices: 1071388--1071643 Score: 309
Period size: 118 Copynumber: 2.2 Consensus size: 114
1071378 GACATTTACA
* * *
1071388 TTTTTTTAC-CTAATTTAGTATTTGAACTTAACACCTTTTTT-TAATTTGTTACCTAAATTTTTT
1 TTTTTTTACTC-AATTTGGTATCTGAACTTAACA-CTTTTTTCTAATTTGGTACCTAAA-TTTTT
* ** * *
1071451 TTGGACTCATTTTGGTACTTGAACTTGTCACTTTTTCCTAATTTGGTACCTAAAT
63 TTGGACTCAATTTCATACCTGAACTTGGCACTTTTTCCTAATTTGGTA---AAAT
*
1071506 TTTTTTTACTCAATTTGGTATCTGAACTTAACATTTTTTTCCTAATTTGGTACCTAAATTTTTTT
1 TTTTTTTACTCAATTTGGTATCTGAACTTAACACTTTTTT-CTAATTTGGTACCTAAATTTTTTT
* * **
1071571 GGACTCAATTTCATACCTGAACTTGGCATTTTTTCTTAATTTGGTAAGCT
65 GGACTCAATTTCATACCTGAACTTGGCACTTTTTCCTAATTTGGTAAAAT
*
1071621 TTTTTTTATTCAATTTGGTATCT
1 TTTTTTTACTCAATTTGGTATCT
1071644 AAATTTATTA
Statistics
Matches: 121, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
115 24 0.20
117 6 0.05
118 75 0.62
119 16 0.13
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (114 bp):
TTTTTTTACTCAATTTGGTATCTGAACTTAACACTTTTTTCTAATTTGGTACCTAAATTTTTTTG
GACTCAATTTCATACCTGAACTTGGCACTTTTTCCTAATTTGGTAAAAT
Found at i:1071601 original size:60 final size:59
Alignment explanation
Indices: 1071429--1071616 Score: 243
Period size: 59 Copynumber: 3.2 Consensus size: 59
1071419 CACCTTTTTT
* * * * *
1071429 TAATTTGTTACCTAAATTTTTTTTGGACTCATTTTGGTACTTGAACTTGTCACTTTTTCC
1 TAATTTGGTACCTAAA-TTTTTTTGGACTCAATTTGGTACCTGAACTTGACATTTTTTCC
* * *
1071489 TAATTTGGTACCTAAATTTTTTT-TACTCAATTTGGTATCTGAACTTAACATTTTTTTCC
1 TAATTTGGTACCTAAATTTTTTTGGACTCAATTTGGTACCTGAACTTGACA-TTTTTTCC
** * *
1071548 TAATTTGGTACCTAAATTTTTTTGGACTCAATTTCATACCTGAACTTGGCATTTTTTCT
1 TAATTTGGTACCTAAATTTTTTTGGACTCAATTTGGTACCTGAACTTGACATTTTTTCC
1071607 TAATTTGGTA
1 TAATTTGGTA
1071617 AGCTTTTTTT
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
58 21 0.19
59 54 0.49
60 36 0.32
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.50
Consensus pattern (59 bp):
TAATTTGGTACCTAAATTTTTTTGGACTCAATTTGGTACCTGAACTTGACATTTTTTCC
Found at i:1071827 original size:31 final size:30
Alignment explanation
Indices: 1071792--1071970 Score: 97
Period size: 31 Copynumber: 6.0 Consensus size: 30
1071782 TTAAAAAAGA
*
1071792 TTAGGTACCAAATTAGGAAAAAGAGTCAAGT
1 TTAGGTACCAAATTA-AAAAAAGAGTCAAGT
* **
1071823 TTAGGTATCAAATTGAATCCAAA-A---AAGT
1 TTAGGTACCAAATT-AA-AAAAAGAGTCAAGT
* * *
1071851 TTAAGTACCAACTTAAAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAAAAAAAGAGTCAAGT
* * *
1071881 TTAGATACCAAATTAGAAAAAAGTGTCAAAT
1 TTAGGTACCAAATTA-AAAAAAGAGTCAAGT
* * *
1071912 TCAAGTACCAAATTTAGTCAAAAA-A---AAGT
1 TTAGGTACCAAA-TTA--AAAAAAGAGTCAAGT
*
1071941 TTAAGTACCAAATTAAAAAAA-AGTCCAAGT
1 TTAGGTACCAAATTAAAAAAAGAGT-CAAGT
1071971 ACCAAATGTT
Statistics
Matches: 112, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
26 9 0.08
27 2 0.02
28 18 0.16
29 14 0.12
30 20 0.18
31 37 0.33
32 7 0.06
33 5 0.04
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (30 bp):
TTAGGTACCAAATTAAAAAAAGAGTCAAGT
Found at i:1071878 original size:58 final size:59
Alignment explanation
Indices: 1071784--1071894 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 59
1071774 AATTAATATT
* * * *
1071784 AAAAAAGATTAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAGGTATCAAATTGAATCC
1 AAAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAGTTTAGATACCAAATTGAATCC
* * *
1071843 AAAAAAGTTTAAGTACCAACTTA-AAAAAAGTGTCAAGTTTAGATACCAAATT
1 AAAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAGTTTAGATACCAAATT
1071895 AGAAAAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 25 0.56
59 20 0.44
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (59 bp):
AAAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAGTTTAGATACCAAATTGAATCC
Found at i:1071883 original size:30 final size:31
Alignment explanation
Indices: 1071847--1071964 Score: 115
Period size: 31 Copynumber: 3.9 Consensus size: 31
1071837 GAATCCAAAA
*
1071847 AAGTTTAAGTACCAACTTA-AAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
1071877 AAGTTT-AGATACCAAATTAGAAAAAAGTGTC
1 AAGTTTAAG-TACCAAATTAGAAAAAAGTGTC
* *
1071908 AAATTCAAGTACCAAATTTAGTCAAAAAA-----
1 AAGTTTAAGTACCAAA-TTAG--AAAAAAGTGTC
*
1071937 AAGTTTAAGTACCAAATTAAAAAAAAGT
1 AAGTTTAAGTACCAAATTAGAAAAAAGT
1071965 CCAAGTACCA
Statistics
Matches: 74, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
26 6 0.08
28 3 0.04
29 16 0.22
30 15 0.20
31 22 0.30
32 6 0.08
34 6 0.08
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:1071924 original size:89 final size:90
Alignment explanation
Indices: 1071792--1071961 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 90
1071782 TTAAAAAAGA
* * * * * * *
1071792 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAGGTATCAAATTGAATC-CAAAAAAGTTTAAG
1 TTAGATACCAAATTAGAAAAAAGAGTCAAATTCAAGTACCAAATTGAATCAAAAAAAAGTTTAAG
*
1071856 TACCAACTTAAAAAAAGTGTCAAGT
66 TACCAAATTAAAAAAAGTGTCAAGT
* * *
1071881 TTAGATACCAAATTAGAAAAAAGTGTCAAATTCAAGTACCAAATTTAGTCAAAAAAAAGTTTAAG
1 TTAGATACCAAATTAGAAAAAAGAGTCAAATTCAAGTACCAAATTGAATCAAAAAAAAGTTTAAG
1071946 TACCAAATTAAAAAAA
66 TACCAAATTAAAAAAA
1071962 AGTCCAAGTA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 41 0.59
90 28 0.41
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (90 bp):
TTAGATACCAAATTAGAAAAAAGAGTCAAATTCAAGTACCAAATTGAATCAAAAAAAAGTTTAAG
TACCAAATTAAAAAAAGTGTCAAGT
Found at i:1071963 original size:24 final size:24
Alignment explanation
Indices: 1071931--1071977 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1071921 AAATTTAGTC
**
1071931 AAAAAAAAGTTTAAGTACCAAATT
1 AAAAAAAAGTCCAAGTACCAAATT
1071955 AAAAAAAAGTCCAAGTACCAAAT
1 AAAAAAAAGTCCAAGTACCAAAT
1071978 GTTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.19
Consensus pattern (24 bp):
AAAAAAAAGTCCAAGTACCAAATT
Found at i:1074098 original size:34 final size:34
Alignment explanation
Indices: 1074060--1074127 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1074050 ATTGTGATAA
1074060 AAATAAACCCATTTTAGATTGCCCTAGATGAAAG
1 AAATAAACCCATTTTAGATTGCCCTAGATGAAAG
1074094 AAATAAACCCATTTTAGATTGCCCTAGATGAAAG
1 AAATAAACCCATTTTAGATTGCCCTAGATGAAAG
1074128 CAAGAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (34 bp):
AAATAAACCCATTTTAGATTGCCCTAGATGAAAG
Found at i:1074358 original size:7 final size:6
Alignment explanation
Indices: 1074345--1074425 Score: 60
Period size: 7 Copynumber: 13.0 Consensus size: 6
1074335 CAATGGTGGA
* *
1074345 AAAGAG AAAGGAG AAAGGG GAAGGG AAAGGGG AAAGGG ATAA--- AAAGGG
1 AAAGGG AAAGG-G AAAGGG AAAGGG AAA-GGG AAAGGG A-AAGGG AAAGGG
*
1074393 GAAGGG AAAGGGG AAAGGGG AAAGGG ATAAGGG
1 AAAGGG AAA-GGG AAA-GGG AAAGGG A-AAGGG
1074426 GCTAATAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
6 27 0.44
7 32 0.52
ACGTcount: A:0.48, C:0.00, G:0.49, T:0.02
Consensus pattern (6 bp):
AAAGGG
Found at i:1074391 original size:36 final size:36
Alignment explanation
Indices: 1074351--1074422 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
1074341 TGGAAAAGAG
*
1074351 AAAGGAGAAAGGGGAA-GGGAAAGGGGAAAGGGATAA
1 AAAGG-GAAAGGGAAAGGGGAAAGGGGAAAGGGATAA
*
1074387 AAAGGGGAAGGGAAAGGGGAAAGGGGAAAGGGATAA
1 AAAGGGAAAGGGAAAGGGGAAAGGGGAAAGGGATAA
1074423 GGGGCTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 8 0.24
36 25 0.76
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (36 bp):
AAAGGGAAAGGGAAAGGGGAAAGGGGAAAGGGATAA
Found at i:1074471 original size:19 final size:18
Alignment explanation
Indices: 1074447--1074502 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 18
1074437 GTACAATGGT
1074447 GGAAAGGAGAAATGGGAAG
1 GGAAAGG-GAAATGGGAAG
1074466 GGAAAGGGGAAATGGGGAAG
1 GGAAA-GGGAAAT-GGGAAG
*
1074486 GGAAAGGGAAAGGGGAA
1 GGAAAGGGAAATGGGAA
1074503 ATGGGGAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.15
19 16 0.47
20 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.04
Consensus pattern (18 bp):
GGAAAGGGAAATGGGAAG
Found at i:1074475 original size:7 final size:7
Alignment explanation
Indices: 1074447--1074510 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
1074437 GTACAATGGT
1074447 GGAAAGG
1 GGAAAGG
* *
1074454 AGAAATG
1 GGAAAGG
1074461 GG-AA-G
1 GGAAAGG
1074466 GGAAAGG
1 GGAAAGG
1074473 GGAAATGG
1 GGAAA-GG
1074481 GG-AA-G
1 GGAAAGG
1074486 GGAAA-G
1 GGAAAGG
1074492 GGAAAGG
1 GGAAAGG
1074499 GGAAATGG
1 GGAAA-GG
1074507 GGAA
1 GGAA
1074511 GAGGTTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
5 6 0.12
6 12 0.25
7 20 0.42
8 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.52, T:0.05
Consensus pattern (7 bp):
GGAAAGG
Done.